9SYR | pdb_00009syr

Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Mechanism of cotranslational modification of histones H2A and H4 by MetAP1 and NatD.

Yudin, D., Jaskolowski, M., Fan, Z., Burg, N., Chandrasekar, S., Lentzsch, A.M., Scaiola, A., Bothe, A., Deuerling, E., Gamerdinger, M., Shan, S.O., Ban, N.

(2025) Sci Adv 11: eaeb1017-eaeb1017

  • DOI: https://doi.org/10.1126/sciadv.aeb1017
  • Primary Citation of Related Structures:  
    9SYR

  • PubMed Abstract: 

    The replication-dependent histones H2A and H4 are among the most highly expressed proteins in eukaryotes during the S phase to ensure packaging of replicated chromosomes. Nearly all newly synthesized H2A and H4 are N-terminally acetylated by N-terminal acetyltransferase D (NatD) following excision of the initiator methionine by methionine aminopeptidases (MetAPs). These modifications influence chromatin function, but how they occur cotranslationally on these exceptionally abundant and small proteins was not understood. Here, we show that the nascent polypeptide-associated complex controls the cotranslational modification of histones H2A and H4 by recruiting NatD and the upstream enzyme MetAP1 to ribosomes. MetAP1 and NatD cooperate on the ribosome to create a confined environment for the efficient sequential modification of the nascent histone chain. Our work provides a mechanistic model for the early steps of histone maturation.

    • Organizational Affiliation: 
    • Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4B [auth Lc]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5C [auth Ld]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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UniProt GroupP46777
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6D [auth Le]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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UniProt GroupQ02878
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13E [auth Lf]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17F [auth Lg]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18G [auth Lh]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19H [auth Li]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aI [auth Lj]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21J [auth Lk]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22K [auth Ll]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23L [auth Lm]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24M [auth Ln]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aN [auth Lo]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26O [auth Lp]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27P [auth Lq]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aQ [auth Lr]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29R [auth Ls]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30S [auth Lt]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31T [auth Lu]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32U [auth Lv]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aV [auth Lw]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34W [auth Lx]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35X [auth Ly]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36Y [auth Lz]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alphaZ [auth Na]238Homo sapiensMutation(s): 0 
Gene Names: NACA, HSD48
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GTEx:  ENSG00000196531 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription factor BTF3AA [auth Nb]162Homo sapiensMutation(s): 0 
Gene Names: BTF3, NACB, OK/SW-cl.8
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GTEx:  ENSG00000145741 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,N-alpha-acetyltransferase 40BA [auth Nd]365Saccharomyces cerevisiae S288C, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: SMT3, YDR510W, D9719.15, NAA40, NAT11, PATT1
EC: 2.3.1.257
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GTEx:  ENSG00000110583 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1CA [auth Nm]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: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8GA [auth SA]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9HA [auth SB]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5IA [auth SC]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11JA [auth SD]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10KA [auth SE]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13LA [auth SF]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14MA [auth SG]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12NA [auth SH]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15OA [auth Sa]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17PA [auth Sb]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16QA [auth Sc]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13RA [auth Sd]152Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000231500 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21SA [auth Se]84Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000171858 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aTA [auth Sf]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12UA [auth Sg]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Small ribosomal subunit protein eS24WA [auth Sh]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19XA [auth Si]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26YA [auth Sj]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27ZA [auth Sk]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20AB [auth Sl]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25BB [auth Sm]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like FUBI-ribosomal protein eS30 fusion proteinCB [auth Sn]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28DB [auth So]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29EB [auth Sp]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41FB [auth Sq]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinGB [auth Sr]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1HB [auth Ss]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2IB [auth St]295Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000168028 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aJB [auth Su]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2KB [auth Sv]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4, X isoformLB [auth Sw]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3MB [auth Sx]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6NB [auth Sy]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7OB [auth Sz]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37QB [auth LA]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38RB [auth LB]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39SB [auth LC]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40TB [auth LD]99Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150991 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aUB [auth LE]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aVB [auth LF]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28WB [auth LG]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15XB [auth LH]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30YB [auth LI]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aZB [auth LJ]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9AC [auth LK]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10BC [auth LM]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147403 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,Small ubiquitin-related modifier 1,Green fluorescent protein,Small ubiquitin-related modifier 1,Histone H4,X-box-binding protein 1,X-box-binding protein 1CC [auth LN]414Aequorea victoria, Brachypodium distachyon, Homo sapiensMutation(s): 0 
Gene Names: GFP, SUMO1, SMT3, SUM1, Os01g0918300, LOC_Os01g68950, OsJ_04555, P0413C03.34-1, P0678F11.1-1, XBP1
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GTEx:  ENSG00000100219 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11DC [auth LO]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13EC [auth LP]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14FC [auth LQ]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8GC [auth La]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3HC [auth Lb]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S rRNAA [auth L1]5,070Homo sapiens
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Entity ID: 30
MoleculeChains LengthOrganismImage
18S rRNADA [auth S1]1,869Homo sapiens
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Entity ID: 31
MoleculeChains LengthOrganismImage
mRNAEA [auth S2]1,824Homo sapiens
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Entity ID: 32
MoleculeChains LengthOrganismImage
tRNAFA [auth S3]76Homo sapiens
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(by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains LengthOrganismImage
5S rRNAVA [auth L2]121Homo sapiens
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 68
MoleculeChains LengthOrganismImage
5.8S rRNAPB [auth L3]157Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA
Download Ideal Coordinates CCD File 
JC [auth Nd]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
GTP
Query on GTP
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MC [auth L2]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IC [auth Lx]
KC [auth Nm]
LC [auth Nm]
NC [auth Sj]
OC [auth Sp]
IC [auth Lx],
KC [auth Nm],
LC [auth Nm],
NC [auth Sj],
OC [auth Sp],
PC [auth Sr],
QC [auth LA],
RC [auth LD],
SC [auth LE],
TC [auth LF]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HY3
Query on HY3		UA [auth Sg]L-PEPTIDE LINKINGC5 H9 N O3PRO
NMM
Query on NMM		XA [auth Si]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101072047
Swiss National Science FoundationSwitzerland310030_212308
Swiss National Science FoundationSwitzerland51NF40-205601
German Research Foundation (DFG)Germany537004599
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM136321

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-14
    Changes: Data collection, Database references