28ZX | pdb_000028zx

human 48S PIC with mRNA (Kozak_1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Macromolecule Content 

  • Total Structure Weight: 2,021.47 kDa 
  • Atom Count: 108,811 
  • Modeled Residue Count: 11,144 
  • Deposited Residue Count: 13,986 
  • Unique protein chains: 47
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L41B [auth Ln]25Homo sapiensMutation(s): 0 
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Find proteins for P62945 (Homo sapiens)
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GTEx:  ENSG00000229117 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4, X isoformC [auth SE]263Homo sapiensMutation(s): 0 
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Find proteins for P62701 (Homo sapiens)
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GTEx:  ENSG00000198034 
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UniProt GroupP62701
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein SAD [auth SA]295Homo sapiensMutation(s): 0 
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Find proteins for P08865 (Homo sapiens)
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PHAROS:  P08865
GTEx:  ENSG00000168028 
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UniProt GroupP08865
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aE [auth SB]264Homo sapiensMutation(s): 0 
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Find proteins for P61247 (Homo sapiens)
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GTEx:  ENSG00000145425 
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UniProt GroupP61247
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7F [auth SH]194Homo sapiensMutation(s): 0 
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Find proteins for P62081 (Homo sapiens)
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PHAROS:  P62081
GTEx:  ENSG00000171863 
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UniProt GroupP62081
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8G [auth SI]208Homo sapiensMutation(s): 0 
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Find proteins for P62241 (Homo sapiens)
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GTEx:  ENSG00000142937 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17H [auth SL]158Homo sapiensMutation(s): 0 
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Find proteins for P62280 (Homo sapiens)
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GTEx:  ENSG00000142534 
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UniProt GroupP62280
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S21I [auth SV]83Homo sapiensMutation(s): 0 
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Find proteins for P63220 (Homo sapiens)
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GTEx:  ENSG00000171858 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23J [auth SX]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S26K [auth Sa]115Homo sapiensMutation(s): 0 
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Find proteins for P62854 (Homo sapiens)
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GTEx:  ENSG00000197728 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2L [auth SC]293Homo sapiensMutation(s): 0 
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Find proteins for P15880 (Homo sapiens)
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PHAROS:  P15880
GTEx:  ENSG00000140988 
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UniProt GroupP15880
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6M [auth SG]249Homo sapiensMutation(s): 0 
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Find proteins for P62753 (Homo sapiens)
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GTEx:  ENSG00000137154 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9N [auth SJ]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13O [auth SN]151Homo sapiensMutation(s): 0 
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Find proteins for P62277 (Homo sapiens)
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PHAROS:  P62277
GTEx:  ENSG00000110700 
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UniProt GroupP62277
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14P [auth SO]151Homo sapiensMutation(s): 0 
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Find proteins for P62263 (Homo sapiens)
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PHAROS:  P62263
GTEx:  ENSG00000164587 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aQ [auth SW]130Homo sapiensMutation(s): 0 
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Find proteins for P62244 (Homo sapiens)
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PHAROS:  P62244
GTEx:  ENSG00000134419 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24R [auth SY]133Homo sapiensMutation(s): 0 
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Find proteins for P62847 (Homo sapiens)
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GTEx:  ENSG00000138326 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27S [auth Sb]84Homo sapiensMutation(s): 0 
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Find proteins for P42677 (Homo sapiens)
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PHAROS:  P42677
GTEx:  ENSG00000177954 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-like FUBI-ribosomal protein eS30 fusion proteinT [auth Se]133Homo sapiensMutation(s): 0 
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Find proteins for P62861 (Homo sapiens)
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PHAROS:  P62861
GTEx:  ENSG00000149806 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3V [auth SD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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Find proteins for P23396 (Homo sapiens)
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PHAROS:  P23396
GTEx:  ENSG00000149273 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S5W [auth SF]204Homo sapiensMutation(s): 0 
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Find proteins for P46782 (Homo sapiens)
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PHAROS:  P46782
GTEx:  ENSG00000083845 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
UbiquitinX [auth Sf]156Homo sapiensMutation(s): 0 
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Find proteins for P62979 (Homo sapiens)
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PHAROS:  P62979
GTEx:  ENSG00000143947 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17Y [auth SR]135Homo sapiensMutation(s): 0 
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Find proteins for P08708 (Homo sapiens)
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PHAROS:  P08708
GTEx:  ENSG00000182774 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29Z [auth Sd]56Homo sapiensMutation(s): 0 
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Find proteins for P62273 (Homo sapiens)
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GTEx:  ENSG00000213741 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1AA [auth Sg]317Homo sapiensMutation(s): 0 
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Find proteins for P63244 (Homo sapiens)
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GTEx:  ENSG00000204628 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28BA [auth Sc]69Homo sapiensMutation(s): 0 
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Find proteins for P62857 (Homo sapiens)
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GTEx:  ENSG00000233927 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S10CA [auth SK]165Homo sapiensMutation(s): 0 
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Find proteins for P46783 (Homo sapiens)
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GTEx:  ENSG00000124614 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12DA [auth SM]132Homo sapiensMutation(s): 0 
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Find proteins for P25398 (Homo sapiens)
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GTEx:  ENSG00000112306 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S20EA [auth SU]119Homo sapiensMutation(s): 0 
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Find proteins for P60866 (Homo sapiens)
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GTEx:  ENSG00000008988 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16FA [auth SQ]146Homo sapiensMutation(s): 0 
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Find proteins for P62249 (Homo sapiens)
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GTEx:  ENSG00000105193 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18GA [auth SS]152Homo sapiensMutation(s): 0 
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Find proteins for P62269 (Homo sapiens)
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GTEx:  ENSG00000231500 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19HA [auth ST]145Homo sapiensMutation(s): 0 
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Find proteins for P39019 (Homo sapiens)
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GTEx:  ENSG00000105372 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15IA [auth SP]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25JA [auth SZ]125Homo sapiensMutation(s): 0 
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Find proteins for P62851 (Homo sapiens)
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GTEx:  ENSG00000118181 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1KA [auth D]315Homo sapiensMutation(s): 0 
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Find proteins for P05198 (Homo sapiens)
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GTEx:  ENSG00000134001 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3LA [auth E]472Homo sapiensMutation(s): 0 
EC: 3.6.5.3
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Find proteins for P41091 (Homo sapiens)
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PHAROS:  P41091
GTEx:  ENSG00000130741 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 2MA [auth F]333Homo sapiensMutation(s): 0 
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Find proteins for P20042 (Homo sapiens)
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PHAROS:  P20042
GTEx:  ENSG00000125977 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1A, X-chromosomalOA [auth H]144Homo sapiensMutation(s): 0 
Gene Names: EIF1AXEIF1AEIF4C
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Find proteins for P47813 (Homo sapiens)
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GTEx:  ENSG00000173674 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EPA [auth e]445Homo sapiensMutation(s): 0 
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Find proteins for P60228 (Homo sapiens)
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GTEx:  ENSG00000104408 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DQA [auth d]548Homo sapiensMutation(s): 0 
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Find proteins for O15371 (Homo sapiens)
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GTEx:  ENSG00000100353 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CRA [auth c]913Homo sapiensMutation(s): 0 
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PHAROS:  Q99613
GTEx:  ENSG00000184110 
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UniProt GroupQ99613
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ASA [auth a]1,382Homo sapiensMutation(s): 0 
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Find proteins for Q14152 (Homo sapiens)
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PHAROS:  Q14152
GTEx:  ENSG00000107581 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FTA [auth 3f]357Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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Find proteins for O00303 (Homo sapiens)
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PHAROS:  O00303
GTEx:  ENSG00000175390 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MUA [auth m]374Homo sapiensMutation(s): 0 
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Find proteins for Q7L2H7 (Homo sapiens)
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PHAROS:  Q7L2H7
GTEx:  ENSG00000149100 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HVA [auth h]352Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15372 (Homo sapiens)
Explore O15372 
Go to UniProtKB:  O15372
PHAROS:  O15372
GTEx:  ENSG00000147677 
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UniProt GroupO15372
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Reference Sequence
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KWA [auth k]218Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ5 (Homo sapiens)
Explore Q9UBQ5 
Go to UniProtKB:  Q9UBQ5
PHAROS:  Q9UBQ5
GTEx:  ENSG00000178982 
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UniProt GroupQ9UBQ5
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Reference Sequence
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LXA [auth l]564Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y262 (Homo sapiens)
Explore Q9Y262 
Go to UniProtKB:  Q9Y262
GTEx:  ENSG00000100129 
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UniProt GroupQ9Y262
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth S2]1,869Homo sapiens
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Reference Sequence
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Entity ID: 21
MoleculeChains LengthOrganismImage
mRNA_KozakU [auth B]50Homo
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Entity ID: 40
MoleculeChains LengthOrganismImage
initiator tRNANA [auth G]75Homo sapiens
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP

Query on GNP



Download:Ideal Coordinates CCD File
BF [auth E]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MET

Query on MET



Download:Ideal Coordinates CCD File
CF [auth E]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
RE [auth Sa],
YE [auth Sf],
ZE [auth Sd]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
AB [auth S2]
AF [auth Sd]
BB [auth S2]
CB [auth S2]
DB [auth S2]
AB [auth S2],
AF [auth Sd],
BB [auth S2],
CB [auth S2],
DB [auth S2],
EB [auth S2],
FB [auth S2],
GB [auth S2],
HB [auth S2],
IB [auth S2],
JB [auth S2],
KB [auth S2],
LB [auth S2],
MB [auth S2],
NB [auth S2],
OB [auth S2],
XE [auth SF],
YA [auth S2],
ZA [auth S2]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AC [auth S2]
AD [auth S2]
AE [auth S2]
BC [auth S2]
BD [auth S2]
AC [auth S2],
AD [auth S2],
AE [auth S2],
BC [auth S2],
BD [auth S2],
BE [auth S2],
CC [auth S2],
CD [auth S2],
CE [auth S2],
DC [auth S2],
DD [auth S2],
DE [auth S2],
DF [auth H],
EC [auth S2],
ED [auth S2],
EE [auth S2],
FC [auth S2],
FD [auth S2],
FE [auth S2],
GC [auth S2],
GD [auth S2],
GE [auth S2],
HC [auth S2],
HD [auth S2],
HE [auth S2],
IC [auth S2],
ID [auth S2],
IE [auth S2],
JC [auth S2],
JD [auth S2],
JE [auth S2],
KC [auth S2],
KD [auth S2],
KE [auth S2],
LC [auth S2],
LD [auth S2],
LE [auth S2],
MC [auth S2],
MD [auth S2],
ME [auth S2],
NC [auth S2],
ND [auth S2],
NE [auth S2],
OC [auth S2],
OD [auth S2],
OE [auth S2],
PB [auth S2],
PC [auth S2],
PD [auth S2],
PE [auth S2],
QB [auth S2],
QC [auth S2],
QD [auth S2],
QE [auth S2],
RB [auth S2],
RC [auth S2],
RD [auth S2],
SB [auth S2],
SC [auth S2],
SD [auth S2],
SE [auth Sa],
TB [auth S2],
TC [auth S2],
TD [auth S2],
TE [auth SN],
UB [auth S2],
UC [auth S2],
UD [auth S2],
UE [auth B],
VB [auth S2],
VC [auth S2],
VD [auth S2],
VE [auth B],
WB [auth S2],
WC [auth S2],
WD [auth S2],
WE [auth B],
XB [auth S2],
XC [auth S2],
XD [auth S2],
YB [auth S2],
YC [auth S2],
YD [auth S2],
ZB [auth S2],
ZC [auth S2],
ZD [auth S2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NMM
Query on NMM
HA [auth ST]L-PEPTIDE LINKINGC7 H16 N4 O2ARG

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.0_5936
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-23-CE11-0003-01
Agence Nationale de la Recherche (ANR)FranceANR 20-SFRI-0012
Laboratories of Excellence (LabEx)FranceANR-10-LABX-0036_NETRNA
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-0005

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-10
    Type: Initial release