8UKB

In situ HHT and CHX treated human hibernating state without E-tRNA 80S ribosome

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-10-12 Released: 2024-11-20 
  • Deposition Author(s): Wei, Z., Yong, X.
  • Funding Organization(s): Not funded

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

In situ human hibernating rotated state 80S ribosome

Wei, Z., Yong, X.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2A [auth CB]856Homo sapiensMutation(s): 0 
EC: 3.6.5
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GTEx:  ENSG00000167658 
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UniProt GroupP13639
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serbp1B [auth CD]55Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142864 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8F [auth LA]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3G [auth LB]402Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4H [auth LC]368Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18I [auth LD]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6J [auth LE]247Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7K [auth LF]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aL [auth LG]241Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9M [auth LH]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL16-likeN [auth LI]213Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11O [auth LJ]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13P [auth LL]210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14Q [auth LM]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15R [auth LN]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aS [auth LO]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17T [auth LP]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18U [auth LQ]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19V [auth LR]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aW [auth LS]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21X [auth LT]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Heparin-binding protein HBp15Y [auth LU]101Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23Z [auth LV]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24AA [auth LW]124Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aBA [auth LX]120Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26CA [auth LY]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27DA [auth LZ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aEA [auth La]147Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29FA [auth Lb]121Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30GA [auth Lc]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31HA [auth Ld]107Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32IA [auth Le]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aJA [auth Lf]109Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34KA [auth Lg]114Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35LA [auth Lh]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36MA [auth Li]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37NA [auth Lj]86Homo sapiensMutation(s): 0 
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Find proteins for P61927 (Homo sapiens)
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GTEx:  ENSG00000145592 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38OA [auth Lk]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39PA [auth Ll]50Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40QA [auth Lm]52Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41RA [auth Ln]24Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aSA [auth Lo]105Homo sapiensMutation(s): 0 
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PHAROS:  P83881
GTEx:  ENSG00000241343 
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UniProt GroupP83881
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aTA [auth Lp]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28UA [auth Lr]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0VA [auth Ls]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089157 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12 [Homo sapiens]WA [auth Lt]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aXA [auth Lz]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAZA [auth SA]221Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aAB [auth SB]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2BB [auth SC]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3CB [auth SD]227Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4, X isoformDB [auth SE]262Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5EB [auth SF]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6FB [auth SG]237Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7GB [auth SH]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8HB [auth SI]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9IB [auth SJ]185Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10JB [auth SK]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11KB [auth SL]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12LB [auth SM]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13MB [auth SN]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11NB [auth SO]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19OB [auth SP]121Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9PB [auth SQ]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17QB [auth SR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18RB [auth SS]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19SB [auth ST]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20TB [auth SU]104Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21UB [auth SV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aVB [auth SW]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23WB [auth SX]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24XB [auth SY]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25YB [auth SZ]75Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26ZB [auth Sa]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27AC [auth Sb]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28BC [auth Sc]64Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29CC [auth Sd]55Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS30DC [auth Se]58Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aEC [auth Sf]67Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1FC [auth Sg]313Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HMT (Subject of Investigation/LOI)
Query on HMT
Download Ideal Coordinates CCD File 
KK [auth L5](3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
C29 H39 N O9
HYFHYPWGAURHIV-JFIAXGOJSA-N
WV3 (Subject of Investigation/LOI)
Query on WV3
Download Ideal Coordinates CCD File 
LK [auth L5]4-{(2R)-2-[(1R,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
AL [auth Lj]
BL [auth Lm]
CL [auth Lo]
DL [auth Lp]
IM [auth Sa]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
AD [auth L5]
AE [auth L5]
AF [auth L5]
AG [auth L5]
AH [auth L5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release