8G60

mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 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

mRNA decoding in human is kinetically and structurally distinct from bacteria.

Holm, M.Natchiar, S.K.Rundlet, E.J.Myasnikov, A.G.Watson, Z.L.Altman, R.B.Wang, H.Y.Taunton, J.Blanchard, S.C.

(2023) Nature 617: 200-207

  • DOI: https://doi.org/10.1038/s41586-023-05908-w
  • Primary Citation of Related Structures:  
    8G5Y, 8G5Z, 8G60, 8G61, 8G6J, 8GLP

  • PubMed Abstract: 

    In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems 1 . Although key features are conserved across evolution 2 , eukaryotes achieve higher-fidelity mRNA decoding than bacteria 3 . In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment 4-6 . Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.


  • Organizational Affiliation

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eS1E [auth SB]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uS2F [auth SA]295Homo sapiensMutation(s): 0 
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PHAROS:  P08865
GTEx:  ENSG00000168028 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uS3G [auth SD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uS4H [auth SJ]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eS4I [auth SE]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uS5J [auth SC]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eS6K [auth SG]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uS7L [auth SF]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eS7M [auth SH]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uS8N [auth SW]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eS8O [auth SI]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS9P [auth SQ]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uS10Q [auth SU]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eS10R [auth SK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uS11S [auth SO]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS12T [auth SX]143Homo sapiensMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eS12U [auth SM]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS13V [auth SS]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uS14W [auth Sd]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS15X [auth SN]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS17Y [auth SL]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eS17Z [auth SR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS19AA [auth SP]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS19BA [auth ST]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eS21CA [auth SV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eS24DA [auth SY]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eS25EA [auth SZ]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS26FA [auth Sa]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eS27GA [auth Sb]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eS28HA [auth Sc]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eS30IA [auth Se]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eS31JA [auth Sf]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1KA [auth Sg]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uL1LA [auth Lz]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uL2MA [auth LA]257Homo sapiensMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
uL3NA [auth LB]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uL4OA [auth LC]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
uL5PA [auth LJ]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
uL6QA [auth LH]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL6RA [auth LE]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL8SA [auth LG]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
uL10TA [auth Lq]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089157 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
uL11UA [auth LK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
uL13VA [auth LO]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
eL13WA [auth LL]270Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uL14XA [auth LV]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
eL14YA [auth LM]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
uL15ZA [auth La]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
eL15AB [auth LN]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uL16BB [auth LI]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147403 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
uL18CB [auth LD]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
eL18DB [auth LQ]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
eL19EB [auth LR]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
eL20FB [auth LS]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
eL21GB [auth LT]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
uL22HB [auth LP]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
eL22IB [auth LU]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uL23JB [auth LX]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uL24KB [auth LY]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
eL24LB [auth LW]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
eL27MB [auth LZ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
eL28NB [auth Lr]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
uL29OB [auth Lh]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eL29PB [auth Lb]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uL30QB [auth LF]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
eL30RB [auth Lc]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
eL31SB [auth Ld]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
eL32TB [auth Le]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
eL33UB [auth Lf]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
eL34VB [auth Lg]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eL36WB [auth Li]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eL37XB [auth Lj]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eL38YB [auth Lk]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
eL39ZB [auth Ll]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
eL40AC [auth Lm]128Homo sapiensMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
eL41BC [auth Ln]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
eL42CC [auth Lo]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
eL43DC [auth Lp]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
eEF1AHC [auth EF]462Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156508 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth S2]1,869Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNAB [auth L8]156Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
28S rRNAC [auth L5]5,069Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth L7]120Homo sapiens
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Entity ID: 83
MoleculeChains LengthOrganismImage
mRNAEC [auth mR]60Homo sapiens
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Entity ID: 84
MoleculeChains LengthOrganismImage
A-site tRNAFC [auth At]76Homo sapiens
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Entity ID: 85
MoleculeChains LengthOrganismImage
P-site tRNAGC [auth Pt]77Homo sapiens
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZIY (Subject of Investigation/LOI)
Query on ZIY

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OV [auth EF]plitidepsin
C57 H87 N7 O15
UUSZLLQJYRSZIS-LXNNNBEUSA-N
GSP
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NV [auth EF]5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
3H3
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QH [auth L5]4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione
C26 H35 N O6
OYOKHBHOTQDIPM-UGGBQLGDSA-N
ANM
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AH [auth L5]ANISOMYCIN
C14 H19 N O4
YKJYKKNCCRKFSL-RDBSUJKOSA-N
PHE
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JV [auth At]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
MET
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MV [auth Pt]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
SPD
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BH [auth L5]
CH [auth L5]
DH [auth L5]
EH [auth L5]
FH [auth L5]
BH [auth L5],
CH [auth L5],
DH [auth L5],
EH [auth L5],
FH [auth L5],
GH [auth L5],
HH [auth L5],
IC [auth S2]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT
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IH [auth L5]
JC [auth S2]
JH [auth L5]
KC [auth S2]
KH [auth L5]
IH [auth L5],
JC [auth S2],
JH [auth L5],
KC [auth S2],
KH [auth L5],
LH [auth L5],
MH [auth L5],
NH [auth L5],
OH [auth L5],
PH [auth L5]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
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BV [auth Lg]
EV [auth Lj]
GV [auth Lm]
HU [auth Sd]
HV [auth Lo]
BV [auth Lg],
EV [auth Lj],
GV [auth Lm],
HU [auth Sd],
HV [auth Lo],
IV [auth Lp],
KU [auth Sa]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AI [auth L5]
RH [auth L5]
SH [auth L5]
TH [auth L5]
UH [auth L5]
AI [auth L5],
RH [auth L5],
SH [auth L5],
TH [auth L5],
UH [auth L5],
VH [auth L5],
WH [auth L5],
XH [auth L5],
YH [auth L5],
ZH [auth L5]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth S2]
AE [auth S2]
AF [auth S2]
AG [auth S2]
AJ [auth L5]
AD [auth S2],
AE [auth S2],
AF [auth S2],
AG [auth S2],
AJ [auth L5],
AK [auth L5],
AL [auth L5],
AM [auth L5],
AN [auth L5],
AO [auth L5],
AP [auth L5],
AQ [auth L5],
AR [auth L5],
AS [auth L5],
AT [auth L5],
AU [auth L7],
AV [auth Lf],
BD [auth S2],
BE [auth S2],
BF [auth S2],
BG [auth S2],
BI [auth L5],
BJ [auth L5],
BK [auth L5],
BL [auth L5],
BM [auth L5],
BN [auth L5],
BO [auth L5],
BP [auth L5],
BQ [auth L5],
BR [auth L5],
BS [auth L5],
BT [auth L5],
BU [auth L7],
CD [auth S2],
CE [auth S2],
CF [auth S2],
CG [auth S2],
CI [auth L5],
CJ [auth L5],
CK [auth L5],
CL [auth L5],
CM [auth L5],
CN [auth L5],
CO [auth L5],
CP [auth L5],
CQ [auth L5],
CR [auth L5],
CS [auth L5],
CT [auth L5],
CU [auth L7],
CV [auth Lg],
DD [auth S2],
DE [auth S2],
DF [auth S2],
DG [auth S2],
DI [auth L5],
DJ [auth L5],
DK [auth L5],
DL [auth L5],
DM [auth L5],
DN [auth L5],
DO [auth L5],
DP [auth L5],
DQ [auth L5],
DR [auth L5],
DS [auth L5],
DT [auth L5],
DU [auth SG],
DV [auth Lg],
ED [auth S2],
EE [auth S2],
EF [auth S2],
EG [auth S2],
EI [auth L5],
EJ [auth L5],
EK [auth L5],
EL [auth L5],
EM [auth L5],
EN [auth L5],
EO [auth L5],
EP [auth L5],
EQ [auth L5],
ER [auth L5],
ES [auth L5],
ET [auth L5],
EU [auth SO],
FD [auth S2],
FE [auth S2],
FF [auth S2],
FG [auth S2],
FI [auth L5],
FJ [auth L5],
FK [auth L5],
FL [auth L5],
FM [auth L5],
FN [auth L5],
FO [auth L5],
FP [auth L5],
FQ [auth L5],
FR [auth L5],
FS [auth L5],
FT [auth L5],
FU [auth SS],
FV [auth Lj],
GD [auth S2],
GE [auth S2],
GF [auth S2],
GG [auth S2],
GI [auth L5],
GJ [auth L5],
GK [auth L5],
GL [auth L5],
GM [auth L5],
GN [auth L5],
GO [auth L5],
GP [auth L5],
GQ [auth L5],
GR [auth L5],
GS [auth L5],
GT [auth L5],
GU [auth SS],
HD [auth S2],
HE [auth S2],
HF [auth S2],
HG [auth S2],
HI [auth L5],
HJ [auth L5],
HK [auth L5],
HL [auth L5],
HM [auth L5],
HN [auth L5],
HO [auth L5],
HP [auth L5],
HQ [auth L5],
HR [auth L5],
HS [auth L5],
HT [auth L5],
ID [auth S2],
IE [auth S2],
IF [auth S2],
IG [auth S2],
II [auth L5],
IJ [auth L5],
IK [auth L5],
IL [auth L5],
IM [auth L5],
IN [auth L5],
IO [auth L5],
IP [auth L5],
IQ [auth L5],
IR [auth L5],
IS [auth L5],
IT [auth L5],
IU [auth SN],
JD [auth S2],
JE [auth S2],
JF [auth S2],
JG [auth S2],
JI [auth L5],
JJ [auth L5],
JK [auth L5],
JL [auth L5],
JM [auth L5],
JN [auth L5],
JO [auth L5],
JP [auth L5],
JQ [auth L5],
JR [auth L5],
JS [auth L5],
JT [auth L5],
JU [auth SP],
KD [auth S2],
KE [auth S2],
KF [auth S2],
KG [auth S2],
KI [auth L5],
KJ [auth L5],
KK [auth L5],
KL [auth L5],
KM [auth L5],
KN [auth L5],
KO [auth L5],
KP [auth L5],
KQ [auth L5],
KR [auth L5],
KS [auth L5],
KT [auth L5],
KV [auth Pt],
LC [auth S2],
LD [auth S2],
LE [auth S2],
LF [auth S2],
LG [auth S2],
LI [auth L5],
LJ [auth L5],
LK [auth L5],
LL [auth L5],
LM [auth L5],
LN [auth L5],
LO [auth L5],
LP [auth L5],
LQ [auth L5],
LR [auth L5],
LS [auth L5],
LT [auth L5],
LU [auth Sa],
LV [auth Pt],
MC [auth S2],
MD [auth S2],
ME [auth S2],
MF [auth S2],
MG [auth S2],
MI [auth L5],
MJ [auth L5],
MK [auth L5],
ML [auth L5],
MM [auth L5],
MN [auth L5],
MO [auth L5],
MP [auth L5],
MQ [auth L5],
MR [auth L5],
MS [auth L5],
MT [auth L5],
MU [auth LA],
NC [auth S2],
ND [auth S2],
NE [auth S2],
NF [auth S2],
NG [auth S2],
NI [auth L5],
NJ [auth L5],
NK [auth L5],
NL [auth L5],
NM [auth L5],
NN [auth L5],
NO [auth L5],
NP [auth L5],
NQ [auth L5],
NR [auth L5],
NS [auth L5],
NT [auth L5],
NU [auth LB],
OC [auth S2],
OD [auth S2],
OE [auth S2],
OF [auth S2],
OG [auth S2],
OI [auth L5],
OJ [auth L5],
OK [auth L5],
OL [auth L5],
OM [auth L5],
ON [auth L5],
OO [auth L5],
OP [auth L5],
OQ [auth L5],
OR [auth L5],
OS [auth L5],
OT [auth L5],
OU [auth LB],
PC [auth S2],
PD [auth S2],
PE [auth S2],
PF [auth S2],
PG [auth S2],
PI [auth L5],
PJ [auth L5],
PK [auth L5],
PL [auth L5],
PM [auth L5],
PN [auth L5],
PO [auth L5],
PP [auth L5],
PQ [auth L5],
PR [auth L5],
PS [auth L5],
PT [auth L5],
PU [auth LB],
PV [auth EF],
QC [auth S2],
QD [auth S2],
QE [auth S2],
QF [auth S2],
QG [auth S2],
QI [auth L5],
QJ [auth L5],
QK [auth L5],
QL [auth L5],
QM [auth L5],
QN [auth L5],
QO [auth L5],
QP [auth L5],
QQ [auth L5],
QR [auth L5],
QS [auth L5],
QT [auth L5],
QU [auth LC],
RC [auth S2],
RD [auth S2],
RE [auth S2],
RF [auth S2],
RG [auth S2],
RI [auth L5],
RJ [auth L5],
RK [auth L5],
RL [auth L5],
RM [auth L5],
RN [auth L5],
RO [auth L5],
RP [auth L5],
RQ [auth L5],
RR [auth L5],
RS [auth L5],
RT [auth L5],
RU [auth LL],
SC [auth S2],
SD [auth S2],
SE [auth S2],
SF [auth S2],
SG [auth S2],
SI [auth L5],
SJ [auth L5],
SK [auth L5],
SL [auth L5],
SM [auth L5],
SN [auth L5],
SO [auth L5],
SP [auth L5],
SQ [auth L5],
SR [auth L5],
SS [auth L5],
ST [auth L5],
SU [auth LV],
TC [auth S2],
TD [auth S2],
TE [auth S2],
TF [auth S2],
TG [auth L8],
TI [auth L5],
TJ [auth L5],
TK [auth L5],
TL [auth L5],
TM [auth L5],
TN [auth L5],
TO [auth L5],
TP [auth L5],
TQ [auth L5],
TR [auth L5],
TS [auth L5],
TT [auth L5],
TU [auth LN],
UC [auth S2],
UD [auth S2],
UE [auth S2],
UF [auth S2],
UG [auth L8],
UI [auth L5],
UJ [auth L5],
UK [auth L5],
UL [auth L5],
UM [auth L5],
UN [auth L5],
UO [auth L5],
UP [auth L5],
UQ [auth L5],
UR [auth L5],
US [auth L5],
UT [auth L5],
UU [auth LI],
VC [auth S2],
VD [auth S2],
VE [auth S2],
VF [auth S2],
VG [auth L8],
VI [auth L5],
VJ [auth L5],
VK [auth L5],
VL [auth L5],
VM [auth L5],
VN [auth L5],
VO [auth L5],
VP [auth L5],
VQ [auth L5],
VR [auth L5],
VS [auth L5],
VT [auth L5],
VU [auth LR],
WC [auth S2],
WD [auth S2],
WE [auth S2],
WF [auth S2],
WG [auth L8],
WI [auth L5],
WJ [auth L5],
WK [auth L5],
WL [auth L5],
WM [auth L5],
WN [auth L5],
WO [auth L5],
WP [auth L5],
WQ [auth L5],
WR [auth L5],
WS [auth L5],
WT [auth L7],
WU [auth LS],
XC [auth S2],
XD [auth S2],
XE [auth S2],
XF [auth S2],
XG [auth L8],
XI [auth L5],
XJ [auth L5],
XK [auth L5],
XL [auth L5],
XM [auth L5],
XN [auth L5],
XO [auth L5],
XP [auth L5],
XQ [auth L5],
XR [auth L5],
XS [auth L5],
XT [auth L7],
XU [auth LP],
YC [auth S2],
YD [auth S2],
YE [auth S2],
YF [auth S2],
YG [auth L8],
YI [auth L5],
YJ [auth L5],
YK [auth L5],
YL [auth L5],
YM [auth L5],
YN [auth L5],
YO [auth L5],
YP [auth L5],
YQ [auth L5],
YR [auth L5],
YS [auth L5],
YT [auth L7],
YU [auth LP],
ZC [auth S2],
ZD [auth S2],
ZE [auth S2],
ZF [auth S2],
ZG [auth L8],
ZI [auth L5],
ZJ [auth L5],
ZK [auth L5],
ZL [auth L5],
ZM [auth L5],
ZN [auth L5],
ZO [auth L5],
ZP [auth L5],
ZQ [auth L5],
ZR [auth L5],
ZS [auth L5],
ZT [auth L7],
ZU [auth Le]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  7 Unique
IDChains TypeFormula2D DiagramParent
SAC
Query on SAC
F [auth SA]L-PEPTIDE LINKINGC5 H9 N O4SER
HY3
Query on HY3
T [auth SX]L-PEPTIDE LINKINGC5 H9 N O3PRO
V5N
Query on V5N
MA [auth LA]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
HIC
Query on HIC
NA [auth LB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
MLZ
Query on MLZ
PB [auth Lb]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
M3L
Query on M3L
AC [auth Lm]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
MLY
Query on MLY
HC [auth EF]L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4092:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations