9F1D

Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

NAC guides a ribosomal multienzyme complex for nascent protein processing.

Lentzsch, A.M., Yudin, D., Gamerdinger, M., Chandrasekar, S., Rabl, L., Scaiola, A., Deuerling, E., Ban, N., Shan, S.O.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07846-7
  • Primary Citation of Related Structures:  
    9F1B, 9F1C, 9F1D

  • PubMed Abstract: 

    Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively 1 . Both modifications are strictly cotranslational and essential in higher eukaryotic organisms 1 . The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex 2,3 (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K 4,5 (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.

    • Organizational Affiliation: 

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21B [auth BT]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29C [auth Bb]245Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12D [auth Bt]165Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17F [auth Aq]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13I [auth Ar]151Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22K [auth BU]128Oryctolagus cuniculusMutation(s): 5 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19L [auth As]145Oryctolagus cuniculusMutation(s): 2 
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2M [auth BA]257Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23N [auth BV]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10O [auth At]119Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3P [auth BB]403Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22Q [auth BP]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26R [auth BY]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aS [auth Av]130Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18T [auth B]297Oryctolagus cuniculusMutation(s): 2 
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Find proteins for G1SZF4 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23U [auth BX]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18V [auth BQ]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27W [auth BZ]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23X [auth Aw]143Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6Y [auth BE]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth BW]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21AA [auth Au]83Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aBA [auth Ba]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CA [auth Ax]130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein uL30DA [auth BF]247Oryctolagus cuniculusMutation(s): 4 
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Find proteins for G1TUB1 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19EA [auth BR]196Oryctolagus cuniculusMutation(s): 3 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2FA [auth AZ]294Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25GA [auth Ay]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8HA [auth BG]266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4IA [auth BC]412Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20JA [auth BS]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aKA [auth Aa]264Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41LA [auth Az]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9MA [auth BH]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1NA [auth EA]386Homo sapiensMutation(s): 1 
Gene Names: METAP1, KIAA0094
EC: 3.4.11.18
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GTEx:  ENSG00000164024 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5OA [auth Ab]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30PA [auth Bc]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10QA [auth BI]214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alphaRA [auth Ct]238Homo sapiensMutation(s): 0 
Gene Names: NACA, HSD48
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GTEx:  ENSG00000196531 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3SA [auth Ac]281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31TA [auth Bd]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11UA [auth BJ]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription factor BTF3VA [auth Cu]162Homo sapiensMutation(s): 0 
Gene Names: BTF3, NACB, OK/SW-cl.8
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GTEx:  ENSG00000145741 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4WA [auth Ad]263Oryctolagus cuniculusMutation(s): 4 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32XA [auth Be]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainYA [auth BK]27Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetyltransferase 50,N-alpha-acetyltransferase 50ZA [auth DA]403Schistosoma japonicum, Homo sapiens
This entity is chimeric		Mutation(s): 0 
EC: 2.5.1.18 (PDB Primary Data), 2.3.1.258 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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PHAROS:  Q9GZZ1
GTEx:  ENSG00000121579 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5AB [auth Ae]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aBB [auth Bf]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13CB [auth BL]211Oryctolagus cuniculusMutation(s): 2 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 15, NatA auxiliary subunit915Homo sapiensMutation(s): 0 
Gene Names: NAA15, GA19, NARG1, NATH, TBDN100
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GTEx:  ENSG00000164134 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6EB [auth Af]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34FB [auth Bg]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14GB [auth BM]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 10HB [auth DC]235Homo sapiensMutation(s): 2 
Gene Names: NAA10, ARD1, ARD1A, TE2
EC: 2.3.1.255
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GTEx:  ENSG00000102030 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7IB [auth Ag]432Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35JB [auth Bh]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15KB [auth BN]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Huntingtin-interacting protein KLB [auth DD]228Homo sapiensMutation(s): 0 
Gene Names: HYPK, C15orf63, HSPC136
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GTEx:  ENSG00000242028 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8MB [auth Ah]208Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36NB [auth Bi]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13OB [auth BO]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9QB [auth Ai]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RB [auth Bj]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27SB [auth AA]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinTB [auth Aj]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth Bk]70Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28VB [auth AB]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11WB [auth Ak]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likeXB [auth Bl]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aYB [auth AC]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12ZB [auth Al]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40 fusion proteinAC [auth Bm]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30BC [auth AD]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13CC [auth Am]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42DC [auth Bo]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26EC [auth AE]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11FC [auth An]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aGC [auth Bp]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1HC [auth AF]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19IC [auth Ao]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28JC [auth Br]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29KC [auth AG]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 90
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9LC [auth Ap]172Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 91
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10MC [auth Bs]318Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S rRNAA [auth B5]4,808Oryctolagus cuniculus
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Entity ID: 5
MoleculeChains LengthOrganismImage
mRNAE [auth AH]3Oryctolagus cuniculus
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S rRNAG [auth B7]120Oryctolagus cuniculus
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Entity ID: 8
MoleculeChains LengthOrganismImage
P-site tRNAH [auth AT]76Oryctolagus cuniculus
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Entity ID: 10
MoleculeChains LengthOrganismImage
5.8S rRNAJ [auth B8]158Oryctolagus cuniculus
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Entity ID: 68
MoleculeChains LengthOrganismImage
18S rRNAPB [auth A2]1,870Oryctolagus cuniculus
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
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KY [auth DB]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
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RW [auth B7]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SPM
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PI [auth B5],
UN [auth B5],
WAA [auth A2]		SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
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BE [auth B5]
BH [auth B5]
BZ [auth A2]
CO [auth B5]
EK [auth B5]
BE [auth B5],
BH [auth B5],
BZ [auth A2],
CO [auth B5],
EK [auth B5],
FV [auth B5],
HAA [auth A2],
ID [auth B5],
IG [auth B5],
IN [auth B5],
IZ [auth A2],
JJ [auth B5],
KU [auth B5],
OC [auth B5],
OM [auth B5],
OT [auth B5],
PAA [auth A2],
PP [auth B5],
PZ [auth A2],
QF [auth B5],
QZ [auth A2],
TL [auth B5],
TS [auth B5],
UY [auth A2],
VH [auth B5],
WE [auth B5],
WO [auth B5],
YK [auth B5],
ZR [auth B5],
ZZ [auth A2]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EFA [auth Bj]
HFA [auth AC]
IFA [auth Bm]
JFA [auth Bo]
LFA [auth AE]
EFA [auth Bj],
HFA [auth AC],
IFA [auth Bm],
JFA [auth Bo],
LFA [auth AE],
LY [auth Bg],
PFA [auth Bp],
QFA [auth AG]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AAA [auth A2]
ACA [auth A2]
ADA [auth A2]
AEA [auth A2]
AF [auth B5]
AAA [auth A2],
ACA [auth A2],
ADA [auth A2],
AEA [auth A2],
AF [auth B5],
AFA [auth A2],
AG [auth B5],
AI [auth B5],
AJ [auth B5],
AL [auth B5],
AM [auth B5],
AP [auth B5],
AS [auth B5],
AT [auth B5],
AU [auth B5],
AY [auth BI],
AZ [auth A2],
BAA [auth A2],
BCA [auth A2],
BDA [auth A2],
BF [auth B5],
BFA [auth A2],
BG [auth B5],
BI [auth B5],
BL [auth B5],
BM [auth B5],
BP [auth B5],
BS [auth B5],
BT [auth B5],
BX [auth B8],
CAA [auth A2],
CBA [auth A2],
CCA [auth A2],
CDA [auth A2],
CE [auth B5],
CF [auth B5],
CH [auth B5],
CI [auth B5],
CL [auth B5],
CM [auth B5],
CP [auth B5],
CS [auth B5],
CT [auth B5],
CX [auth B8],
CY [auth Ct],
CZ [auth A2],
DAA [auth A2],
DBA [auth A2],
DE [auth B5],
DEA [auth A2],
DF [auth B5],
DFA [auth A2],
DH [auth B5],
DI [auth B5],
DL [auth B5],
DM [auth B5],
DO [auth B5],
DP [auth B5],
DQ [auth B5],
DR [auth B5],
DS [auth B5],
DT [auth B5],
DX [auth B8],
DZ [auth A2],
EBA [auth A2],
EE [auth B5],
EEA [auth A2],
EF [auth B5],
EH [auth B5],
EI [auth B5],
EL [auth B5],
EM [auth B5],
EO [auth B5],
EP [auth B5],
ER [auth B5],
ES [auth B5],
ET [auth B5],
EX [auth B8],
EZ [auth A2],
FBA [auth A2],
FCA [auth A2],
FE [auth B5],
FEA [auth A2],
FF [auth B5],
FFA [auth Bj],
FH [auth B5],
FI [auth B5],
FK [auth B5],
FL [auth B5],
FO [auth B5],
FP [auth B5],
FR [auth B5],
FS [auth B5],
FT [auth B5],
FW [auth B7],
FX [auth B8],
FY [auth Be],
GAA [auth A2],
GBA [auth A2],
GCA [auth A2],
GDA [auth A2],
GE [auth B5],
GEA [auth A2],
GF [auth B5],
GH [auth B5],
GI [auth B5],
GK [auth B5],
GL [auth B5],
GO [auth B5],
GP [auth B5],
GR [auth B5],
GS [auth B5],
GU [auth B5],
GV [auth B5],
GW [auth B7],
GX [auth B8],
HCA [auth A2],
HDA [auth A2],
HE [auth B5],
HF [auth B5],
HH [auth B5],
HK [auth B5],
HL [auth B5],
HO [auth B5],
HR [auth B5],
HS [auth B5],
HV [auth B5],
HW [auth B7],
HX [auth B8],
HZ [auth A2],
IAA [auth A2],
ICA [auth A2],
IDA [auth A2],
IE [auth B5],
IF [auth B5],
IH [auth B5],
IK [auth B5],
IL [auth B5],
IO [auth B5],
IR [auth B5],
IS [auth B5],
IV [auth B5],
IW [auth B7],
IX [auth B8],
JAA [auth A2],
JBA [auth A2],
JD [auth B5],
JE [auth B5],
JEA [auth A2],
JG [auth B5],
JH [auth B5],
JK [auth B5],
JL [auth B5],
JN [auth B5],
JO [auth B5],
JQ [auth B5],
JR [auth B5],
JS [auth B5],
JV [auth B5],
JW [auth B7],
JZ [auth A2],
KAA [auth A2],
KBA [auth A2],
KD [auth B5],
KE [auth B5],
KEA [auth A2],
KG [auth B5],
KH [auth B5],
KJ [auth B5],
KK [auth B5],
KN [auth B5],
KO [auth B5],
KQ [auth B5],
KR [auth B5],
KS [auth B5],
KV [auth B5],
KW [auth B7],
KZ [auth A2],
LBA [auth A2],
LD [auth B5],
LEA [auth A2],
LG [auth B5],
LH [auth B5],
LJ [auth B5],
LK [auth B5],
LN [auth B5],
LO [auth B5],
LQ [auth B5],
LR [auth B5],
LU [auth B5],
LV [auth B5],
LW [auth B7],
LZ [auth A2],
MAA [auth A2],
MBA [auth A2],
MCA [auth A2],
MD [auth B5],
MDA [auth A2],
ME [auth B5],
MEA [auth A2],
MG [auth B5],
MH [auth B5],
MJ [auth B5],
MK [auth B5],
MN [auth B5],
MO [auth B5],
MQ [auth B5],
MR [auth B5],
MU [auth B5],
MV [auth B5],
MW [auth B7],
NAA [auth A2],
NBA [auth A2],
NCA [auth A2],
ND [auth B5],
NDA [auth A2],
NE [auth B5],
NEA [auth A2],
NG [auth B5],
NJ [auth B5],
NK [auth B5],
NN [auth B5],
NQ [auth B5],
NR [auth B5],
NU [auth B5],
NV [auth B5],
NY [auth A2],
OAA [auth A2],
OBA [auth A2],
OCA [auth A2],
OD [auth B5],
ODA [auth A2],
OFA [auth An],
OG [auth B5],
OJ [auth B5],
OK [auth B5],
ON [auth B5],
OQ [auth B5],
OR [auth B5],
OS [auth B5],
OU [auth B5],
OV [auth B5],
OY [auth A2],
OZ [auth A2],
PBA [auth A2],
PC [auth B5],
PCA [auth A2],
PD [auth B5],
PG [auth B5],
PJ [auth B5],
PK [auth B5],
PM [auth B5],
PN [auth B5],
PQ [auth B5],
PR [auth B5],
PT [auth B5],
PU [auth B5],
PV [auth B5],
PY [auth A2],
QAA [auth A2],
QC [auth B5],
QD [auth B5],
QEA [auth A2],
QG [auth B5],
QI [auth B5],
QJ [auth B5],
QM [auth B5],
QN [auth B5],
QP [auth B5],
QQ [auth B5],
QT [auth B5],
QU [auth B5],
QV [auth B5],
QW [auth B7],
QX [auth BV],
QY [auth A2],
RAA [auth A2],
RBA [auth A2],
RC [auth B5],
RD [auth B5],
REA [auth A2],
RF [auth B5],
RG [auth B5],
RI [auth B5],
RJ [auth B5],
RM [auth B5],
RN [auth B5],
RP [auth B5],
RQ [auth B5],
RT [auth B5],
RU [auth B5],
RV [auth B5],
RZ [auth A2],
SAA [auth A2],
SBA [auth A2],
SC [auth B5],
SD [auth B5],
SDA [auth A2],
SEA [auth A2],
SF [auth B5],
SG [auth B5],
SI [auth B5],
SJ [auth B5],
SM [auth B5],
SN [auth B5],
SP [auth B5],
SQ [auth B5],
ST [auth B5],
SU [auth B5],
SZ [auth A2],
TBA [auth A2],
TC [auth B5],
TCA [auth A2],
TD [auth B5],
TDA [auth A2],
TEA [auth A2],
TF [auth B5],
TG [auth B5],
TI [auth B5],
TJ [auth B5],
TM [auth B5],
TP [auth B5],
TQ [auth B5],
TT [auth B5],
TU [auth B5],
TY [auth A2],
TZ [auth A2],
UAA [auth A2],
UBA [auth A2],
UC [auth B5],
UCA [auth A2],
UDA [auth A2],
UEA [auth A2],
UF [auth B5],
UI [auth B5],
UJ [auth B5],
UL [auth B5],
UM [auth B5],
UO [auth B5],
UP [auth B5],
UQ [auth B5],
US [auth B5],
UT [auth B5],
UU [auth B5],
UW [auth AT],
UX [auth BP],
UZ [auth A2],
VC [auth B5],
VCA [auth A2],
VF [auth B5],
VI [auth B5],
VL [auth B5],
VM [auth B5],
VP [auth B5],
VR [auth B5],
VS [auth B5],
VT [auth B5],
VU [auth B5],
VW [auth AT],
VY [auth A2],
WC [auth B5],
WCA [auth A2],
WF [auth B5],
WH [auth B5],
WI [auth B5],
WL [auth B5],
WM [auth B5],
WP [auth B5],
WS [auth B5],
WT [auth B5],
WY [auth A2],
XAA [auth A2],
XC [auth B5],
XDA [auth A2],
XE [auth B5],
XEA [auth A2],
XF [auth B5],
XH [auth B5],
XI [auth B5],
XL [auth B5],
XM [auth B5],
XO [auth B5],
XP [auth B5],
XS [auth B5],
XT [auth B5],
XU [auth B5],
XY [auth A2],
XZ [auth A2],
YAA [auth A2],
YBA [auth A2],
YC [auth B5],
YDA [auth A2],
YEA [auth A2],
YF [auth B5],
YH [auth B5],
YI [auth B5],
YL [auth B5],
YM [auth B5],
YO [auth B5],
YP [auth B5],
YS [auth B5],
YT [auth B5],
YX [auth Ba],
YZ [auth A2],
ZAA [auth A2],
ZBA [auth A2],
ZC [auth B5],
ZDA [auth A2],
ZE [auth B5],
ZEA [auth A2],
ZF [auth B5],
ZH [auth B5],
ZI [auth B5],
ZK [auth B5],
ZL [auth B5],
ZM [auth B5],
ZO [auth B5],
ZP [auth B5],
ZS [auth B5],
ZT [auth B5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX
Download Ideal Coordinates CCD File 
ABA [auth A2]
AD [auth B5]
AE [auth B5]
AH [auth B5]
AK [auth B5]
ABA [auth A2],
AD [auth B5],
AE [auth B5],
AH [auth B5],
AK [auth B5],
AN [auth B5],
AO [auth B5],
AQ [auth B5],
AR [auth B5],
AV [auth B5],
AW [auth BT],
AX [auth B8],
BBA [auth A2],
BD [auth B5],
BEA [auth A2],
BJ [auth B5],
BK [auth B5],
BN [auth B5],
BO [auth B5],
BQ [auth B5],
BR [auth B5],
BU [auth B5],
BV [auth B5],
BW [auth BT],
BY [auth BI],
CD [auth B5],
CEA [auth A2],
CFA [auth A2],
CG [auth B5],
CJ [auth B5],
CK [auth B5],
CN [auth B5],
CQ [auth B5],
CR [auth B5],
CU [auth B5],
CV [auth B5],
CW [auth Bb],
DCA [auth A2],
DD [auth B5],
DDA [auth A2],
DG [auth B5],
DJ [auth B5],
DK [auth B5],
DN [auth B5],
DU [auth B5],
DV [auth B5],
DW [auth Bb],
DY [auth Ad],
EAA [auth A2],
ECA [auth A2],
ED [auth B5],
EDA [auth A2],
EG [auth B5],
EJ [auth B5],
EN [auth B5],
EQ [auth B5],
EU [auth B5],
EV [auth B5],
EW [auth B7],
EY [auth Be],
FAA [auth A2],
FD [auth B5],
FDA [auth A2],
FG [auth B5],
FJ [auth B5],
FM [auth B5],
FN [auth B5],
FQ [auth B5],
FU [auth B5],
FZ [auth A2],
GD [auth B5],
GFA [auth Ak],
GG [auth B5],
GJ [auth B5],
GM [auth B5],
GN [auth B5],
GQ [auth B5],
GT [auth B5],
GY [auth Be],
GZ [auth A2],
HBA [auth A2],
HD [auth B5],
HEA [auth A2],
HG [auth B5],
HI [auth B5],
HJ [auth B5],
HM [auth B5],
HN [auth B5],
HP [auth B5],
HQ [auth B5],
HT [auth B5],
HU [auth B5],
HY [auth Be],
IBA [auth A2],
IEA [auth A2],
II [auth B5],
IJ [auth B5],
IM [auth B5],
IP [auth B5],
IQ [auth B5],
IT [auth B5],
IU [auth B5],
IY [auth Bf],
JCA [auth A2],
JDA [auth A2],
JF [auth B5],
JI [auth B5],
JM [auth B5],
JP [auth B5],
JT [auth B5],
JU [auth B5],
JX [auth B8],
JY [auth BL],
KCA [auth A2],
KDA [auth A2],
KF [auth B5],
KFA [auth Bo],
KI [auth B5],
KL [auth B5],
KM [auth B5],
KP [auth B5],
KT [auth B5],
KX [auth B8],
LAA [auth A2],
LCA [auth A2],
LDA [auth A2],
LE [auth B5],
LF [auth B5],
LI [auth B5],
LL [auth B5],
LM [auth B5],
LP [auth B5],
LS [auth B5],
LT [auth B5],
LX [auth B8],
MF [auth B5],
MFA [auth AE],
MI [auth B5],
ML [auth B5],
MM [auth B5],
MP [auth B5],
MS [auth B5],
MT [auth B5],
MX [auth BA],
MY [auth BN],
MZ [auth A2],
NC [auth B5],
NF [auth B5],
NFA [auth An],
NH [auth B5],
NI [auth B5],
NL [auth B5],
NM [auth B5],
NO [auth B5],
NP [auth B5],
NS [auth B5],
NT [auth B5],
NW [auth B7],
NX [auth BA],
NZ [auth A2],
OE [auth B5],
OEA [auth A2],
OF [auth B5],
OH [auth B5],
OI [auth B5],
OL [auth B5],
OO [auth B5],
OP [auth B5],
OW [auth B7],
OX [auth BA],
PDA [auth A2],
PE [auth B5],
PEA [auth A2],
PF [auth B5],
PH [auth B5],
PL [auth B5],
PO [auth B5],
PS [auth B5],
PW [auth B7],
PX [auth BA],
QBA [auth A2],
QCA [auth A2],
QDA [auth A2],
QE [auth B5],
QH [auth B5],
QK [auth B5],
QL [auth B5],
QO [auth B5],
QR [auth B5],
QS [auth B5],
RCA [auth A2],
RDA [auth A2],
RE [auth B5],
RH [auth B5],
RK [auth B5],
RL [auth B5],
RO [auth B5],
RR [auth B5],
RS [auth B5],
RX [auth BB],
RY [auth A2],
SCA [auth A2],
SE [auth B5],
SH [auth B5],
SK [auth B5],
SL [auth B5],
SO [auth B5],
SR [auth B5],
SS [auth B5],
SV [auth B5],
SW [auth B7],
SX [auth BB],
SY [auth A2],
TAA [auth A2],
TE [auth B5],
TH [auth B5],
TK [auth B5],
TN [auth B5],
TO [auth B5],
TR [auth B5],
TV [auth B5],
TW [auth B7],
TX [auth BB],
UD [auth B5],
UE [auth B5],
UG [auth B5],
UH [auth B5],
UK [auth B5],
UR [auth B5],
UV [auth B5],
VAA [auth A2],
VBA [auth A2],
VD [auth B5],
VDA [auth A2],
VE [auth B5],
VEA [auth A2],
VG [auth B5],
VJ [auth B5],
VK [auth B5],
VN [auth B5],
VO [auth B5],
VQ [auth B5],
VV [auth B5],
VX [auth BY],
VZ [auth A2],
WBA [auth A2],
WD [auth B5],
WDA [auth A2],
WEA [auth A2],
WG [auth B5],
WJ [auth B5],
WK [auth B5],
WN [auth B5],
WQ [auth B5],
WR [auth B5],
WU [auth B5],
WV [auth B5],
WW [auth AT],
WX [auth BQ],
WZ [auth A2],
XBA [auth A2],
XCA [auth A2],
XD [auth B5],
XG [auth B5],
XJ [auth B5],
XK [auth B5],
XN [auth B5],
XQ [auth B5],
XR [auth B5],
XV [auth B5],
XW [auth AT],
XX [auth BQ],
YCA [auth A2],
YD [auth B5],
YE [auth B5],
YG [auth B5],
YJ [auth B5],
YN [auth B5],
YQ [auth B5],
YR [auth B5],
YU [auth B5],
YV [auth B5],
YW [auth B8],
YY [auth A2],
ZCA [auth A2],
ZD [auth B5],
ZG [auth B5],
ZJ [auth B5],
ZN [auth B5],
ZQ [auth B5],
ZU [auth B5],
ZV [auth B5],
ZW [auth B8],
ZX [auth BH],
ZY [auth A2]
UNKNOWN ATOM OR ION
X
Modified Residues  8 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ		C [auth Bb]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
SAC
Query on SAC		I [auth Ar]L-PEPTIDE LINKINGC5 H9 N O4SER
NMM
Query on NMM		L [auth As]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
V5N
Query on V5N		M [auth BA]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
HIC
Query on HIC		P [auth BB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
HY3
Query on HY3		X [auth Aw]L-PEPTIDE LINKINGC5 H9 N O3PRO
AYA
Query on AYA		IA [auth BC]L-PEPTIDE LINKINGC5 H9 N O3ALA
M3L
Query on M3L		AC [auth Bm]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesR35 GM136321
German Research Foundation (DFG)GermanySFB969/A01 and A07
Swiss National Science FoundationSwitzerland310030_212308
Swiss National Science FoundationSwitzerland51NF40-205601
European Research Council (ERC)European UnionSynergy Grant 101072047

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 2.0: 2024-09-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary