7QI5

Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2021-12-14 Released: 2023-07-05 
  • Deposition Author(s): Singh, V., Itoh, Y., Amunts, A.
  • Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation, European Research Council (ERC), European Molecular Biology Organization (EMBO), H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.

Singh, V.Itoh, Y.Del'Olio, S.Hassan, A.Naschberger, A.Flygaard, R.K.Nobe, Y.Izumikawa, K.Aibara, S.Andrell, J.Whitford, P.C.Barrientos, A.Taoka, M.Amunts, A.

(2024) Nat Commun 15: 4272-4272

  • DOI: https://doi.org/10.1038/s41467-024-48163-x
  • Primary Citation of Related Structures:  
    7QI4, 7QI5, 7QI6

  • PubMed Abstract: 

    The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA Val . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialB [auth AB]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122140 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialC [auth AC]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialD [auth AD]430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialE [auth AE]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialF [auth AF]242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialG [auth AG]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialH [auth AH]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialI [auth AI]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181991 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialJ [auth AJ]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialK [auth AK]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialL [auth AL]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialM [auth AM]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialN [auth AN]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialO [auth AO]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialP [auth AP]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
MRPS21 isoform 1Q [auth AQ]87Homo sapiensMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialR [auth AR]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialS [auth AS]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialT [auth AT]173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialU [auth AU]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialV [auth AV]414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialW [auth AW]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialX [auth AX]398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialY [auth AY]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialZ [auth AZ]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialAA [auth A0]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialBA [auth A1]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1CA [auth A2]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172586 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinDA [auth A3]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialEA [auth A4]689Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialLA [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialMA [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialNA [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialOA [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialPA [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialQA [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialRA [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialSA [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialTA [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialUA [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialVA [auth P]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialWA [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialXA [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialYA [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialZA [auth T]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialAB [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialBB [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialCB [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialDB [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialEB [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialFB [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialGB [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialHB [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialIB [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialJB [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialKB [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialLB [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialMB [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialNB [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialOB [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialPB [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialQB [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL43RB [auth b]215Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000055950 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialSB [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialTB [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialUB [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialVB [auth f]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialWB [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialXB [auth h]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialYB [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialZB [auth j]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172590 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialAC [auth k]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204822 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialBC [auth l]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183617 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialCC [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialDC [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialEC [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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GTEx:  ENSG00000167862 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1FC [auth q]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179271 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialGC [auth r]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096080 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialHC [auth s]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L12, mitochondrial198Homo sapiensMutation(s): 0 
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Find proteins for P52815 (Homo sapiens)
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Go to UniProtKB:  P52815
PHAROS:  P52815
GTEx:  ENSG00000262814 
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UniProt GroupP52815
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialOC [auth H]267Homo sapiensMutation(s): 0 
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Find proteins for Q9BYD2 (Homo sapiens)
Explore Q9BYD2 
Go to UniProtKB:  Q9BYD2
PHAROS:  Q9BYD2
GTEx:  ENSG00000143436 
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UniProt GroupQ9BYD2
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L1, mitochondrialPC [auth z]325Homo sapiensMutation(s): 0 
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Find proteins for Q9BYD6 (Homo sapiens)
Explore Q9BYD6 
Go to UniProtKB:  Q9BYD6
PHAROS:  Q9BYD6
GTEx:  ENSG00000169288 
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UniProt GroupQ9BYD6
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Entity ID: 1
MoleculeChains LengthOrganismImage
12S mitochondrial rRNAA [auth AA]954Homo sapiens
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Entity ID: 32
MoleculeChains LengthOrganismImage
A/A-tRNAFA [auth Aw]68Homo sapiens
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Entity ID: 33
MoleculeChains LengthOrganismImage
P/P-tRNAGA [auth Ax]70Homo sapiens
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Entity ID: 34
MoleculeChains LengthOrganismImage
E/E-tRNAHA [auth Ay]70Homo sapiens
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Entity ID: 35
MoleculeChains LengthOrganismImage
mRNAIA [auth Az]34Homo sapiens
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Entity ID: 36
MoleculeChains LengthOrganismImage
16S mitochondrial rRNAJA [auth A]1,561Homo sapiens
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Entity ID: 37
MoleculeChains LengthOrganismImage
mitochondrial tRNAValKA [auth B]72Homo sapiens
Sequence Annotations
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
QC [auth AA]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ATP
Query on ATP

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AG [auth AX]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP
Query on GDP

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CG [auth AX]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SPM
Query on SPM

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RC [auth AA]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
FES
Query on FES

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HN [auth r],
YF [auth AP],
ZF [auth AT]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SPD
Query on SPD

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EG [auth A],
FG [auth A],
GG [auth A],
SC [auth AA]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
VAL
Query on VAL

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TM [auth B]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
PUT
Query on PUT

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HG [auth A]1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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AN [auth 0],
CN [auth 4],
XF [auth AO]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AM [auth A]
BM [auth A]
BN [auth 3]
CM [auth A]
DM [auth A]
AM [auth A],
BM [auth A],
BN [auth 3],
CM [auth A],
DM [auth A],
DN [auth 6],
EF [auth AA],
EM [auth A],
FF [auth AA],
FM [auth A],
FN [auth i],
GF [auth AA],
GM [auth A],
GN [auth o],
HF [auth AA],
HM [auth A],
IF [auth AA],
IM [auth A],
JF [auth AA],
JM [auth A],
KF [auth AA],
KM [auth A],
LF [auth AA],
LM [auth A],
MF [auth AA],
MM [auth A],
NF [auth AA],
NM [auth A],
OF [auth AA],
OM [auth A],
PF [auth AA],
PM [auth A],
QF [auth AA],
QL [auth A],
QM [auth A],
RF [auth AA],
RL [auth A],
RM [auth A],
SF [auth AA],
SL [auth A],
SM [auth A],
TF [auth AA],
TL [auth A],
UF [auth AA],
UL [auth A],
VF [auth AA],
VL [auth A],
WL [auth A],
WM [auth D],
XL [auth A],
YL [auth A],
YM [auth M],
ZL [auth A],
ZM [auth W]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth AA]
AE [auth AA]
AF [auth AA]
AH [auth A]
AI [auth A]
AD [auth AA],
AE [auth AA],
AF [auth AA],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth A],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth AX],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth A],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth A],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth A3],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth A],
ED [auth AA],
EE [auth AA],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth A],
EN [auth g],
FD [auth AA],
FE [auth AA],
FH [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
FL [auth A],
GD [auth AA],
GE [auth AA],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth A],
HD [auth AA],
HE [auth AA],
HH [auth A],
HI [auth A],
HJ [auth A],
HK [auth A],
HL [auth A],
ID [auth AA],
IE [auth AA],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth A],
JD [auth AA],
JE [auth AA],
JG [auth A],
JH [auth A],
JI [auth A],
JJ [auth A],
JK [auth A],
JL [auth A],
KD [auth AA],
KE [auth AA],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth A],
LD [auth AA],
LE [auth AA],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
LL [auth A],
MD [auth AA],
ME [auth AA],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
ML [auth A],
ND [auth AA],
NE [auth AA],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
NL [auth A],
OD [auth AA],
OE [auth AA],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth A],
PD [auth AA],
PE [auth AA],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
PL [auth A],
QD [auth AA],
QE [auth AA],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
RD [auth AA],
RE [auth AA],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
SD [auth AA],
SE [auth AA],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
TC [auth AA],
TD [auth AA],
TE [auth AA],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
UC [auth AA],
UD [auth AA],
UE [auth AA],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UM [auth D],
VC [auth AA],
VD [auth AA],
VE [auth AA],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
VM [auth D],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth AB],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
XC [auth AA],
XD [auth AA],
XE [auth AA],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth A],
XM [auth E],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth A],
ZC [auth AA],
ZD [auth AA],
ZE [auth AA],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
Q [auth AQ]L-PEPTIDE LINKINGC5 H9 N O3ALA
SAC
Query on SAC
QA [auth K]L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilEuropean Union--
Knut and Alice Wallenberg FoundationEuropean Union--
European Research Council (ERC)European Union--
European Molecular Biology Organization (EMBO)European Union--
H2020 Marie Curie Actions of the European CommissionEuropean Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-08-09
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-17
    Changes: Structure summary
  • Version 2.2: 2024-04-24
    Changes: Data collection
  • Version 3.0: 2024-06-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 3.1: 2024-07-31
    Changes: Data collection, Database references