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 9QET | pdb_00009qet

Human pre-60S - State 1B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9QET

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

Literature

Human pre-60S - State 1B

Thoms, M., Hurt, E., Beckmann, R.

To be published.

Macromolecule Content 

  • Total Structure Weight: 2,818.46 kDa 
  • Atom Count: 114,018 
  • Modeled Residue Count: 10,023 
  • Deposited Residue Count: 14,844 
  • Unique protein chains: 38
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6A [auth CA]245Homo sapiensMutation(s): 0 
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Find proteins for P56537 (Homo sapiens)
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PHAROS:  P56537
GTEx:  ENSG00000242372 
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UniProt GroupP56537
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2B [auth CB]731Homo sapiensMutation(s): 0 
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Find proteins for Q13823 (Homo sapiens)
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PHAROS:  Q13823
GTEx:  ENSG00000134697 
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UniProt GroupQ13823
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein-like 3C [auth CC]549Homo sapiensMutation(s): 0 
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Find proteins for Q9BVP2 (Homo sapiens)
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PHAROS:  Q9BVP2
GTEx:  ENSG00000163938 
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UniProt GroupQ9BVP2
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding protein 4D [auth CD]634Homo sapiensMutation(s): 0 
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Find proteins for Q9BZE4 (Homo sapiens)
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PHAROS:  Q9BZE4
GTEx:  ENSG00000107937 
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UniProt GroupQ9BZE4
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein LLP homologE [auth CE]129Homo sapiensMutation(s): 0 
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Find proteins for Q9BRT6 (Homo sapiens)
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PHAROS:  Q9BRT6
GTEx:  ENSG00000139233 
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UniProt GroupQ9BRT6
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologF [auth CF]239Homo sapiensMutation(s): 0 
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Find proteins for Q9UKD2 (Homo sapiens)
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PHAROS:  Q9UKD2
GTEx:  ENSG00000053372 
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UniProt GroupQ9UKD2
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Notchless protein homolog 1G [auth CG]485Homo sapiensMutation(s): 1 
Gene Names: NLE1, HUSSY-07
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Find proteins for Q9NVX2 (Homo sapiens)
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GTEx:  ENSG00000073536 
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UniProt GroupQ9NVX2
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2 homologH [auth CH]260Homo sapiensMutation(s): 0 
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Find proteins for O95478 (Homo sapiens)
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GTEx:  ENSG00000164346 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24I [auth CI]163Homo sapiensMutation(s): 0 
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Find proteins for Q9UHA3 (Homo sapiens)
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GTEx:  ENSG00000137876 
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UniProt GroupQ9UHA3
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome production factor 2 homologJ [auth CJ]306Homo sapiensMutation(s): 0 
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Find proteins for Q9H7B2 (Homo sapiens)
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PHAROS:  Q9H7B2
GTEx:  ENSG00000197498 
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UniProt GroupQ9H7B2
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome biogenesis regulatory protein homologK [auth CK]365Homo sapiensMutation(s): 0 
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Find proteins for Q15050 (Homo sapiens)
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PHAROS:  Q15050
GTEx:  ENSG00000179041 
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UniProt GroupQ15050
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3O [auth LB]403Homo sapiensMutation(s): 0 
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Find proteins for P39023 (Homo sapiens)
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GTEx:  ENSG00000100316 
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UniProt GroupP39023
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4P [auth LC]427Homo sapiensMutation(s): 0 
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Find proteins for P36578 (Homo sapiens)
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GTEx:  ENSG00000174444 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5Q [auth LD]297Homo sapiensMutation(s): 0 
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Find proteins for P46777 (Homo sapiens)
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GTEx:  ENSG00000122406 
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UniProt GroupP46777
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6R [auth LE]288Homo sapiensMutation(s): 0 
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Find proteins for Q02878 (Homo sapiens)
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GTEx:  ENSG00000089009 
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UniProt GroupQ02878
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30S [auth LF]248Homo sapiensMutation(s): 0 
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Find proteins for P18124 (Homo sapiens)
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GTEx:  ENSG00000147604 
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UniProt GroupP18124
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aT [auth LG]266Homo sapiensMutation(s): 0 
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Find proteins for P62424 (Homo sapiens)
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GTEx:  ENSG00000148303 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9U [auth LH]192Homo sapiensMutation(s): 0 
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Find proteins for P32969 (Homo sapiens)
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PHAROS:  P32969
GTEx:  ENSG00000163682 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11V [auth LJ]178Homo sapiensMutation(s): 0 
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Find proteins for P62913 (Homo sapiens)
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PHAROS:  P62913
GTEx:  ENSG00000142676 
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UniProt GroupP62913
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13W [auth LL]211Homo sapiensMutation(s): 0 
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Find proteins for P26373 (Homo sapiens)
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PHAROS:  P26373
GTEx:  ENSG00000167526 
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UniProt GroupP26373
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14X [auth LM]215Homo sapiensMutation(s): 0 
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Find proteins for P50914 (Homo sapiens)
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PHAROS:  P50914
GTEx:  ENSG00000188846 
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UniProt GroupP50914
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L15Y [auth LN]204Homo sapiensMutation(s): 0 
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Find proteins for P61313 (Homo sapiens)
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PHAROS:  P61313
GTEx:  ENSG00000174748 
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UniProt GroupP61313
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aZ [auth LO]203Homo sapiensMutation(s): 0 
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Find proteins for P40429 (Homo sapiens)
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PHAROS:  P40429
GTEx:  ENSG00000142541 
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UniProt GroupP40429
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L17AA [auth LP]184Homo sapiensMutation(s): 0 
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Find proteins for P18621 (Homo sapiens)
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PHAROS:  P18621
GTEx:  ENSG00000265681 
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UniProt GroupP18621
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18BA [auth LQ]188Homo sapiensMutation(s): 0 
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Find proteins for Q07020 (Homo sapiens)
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PHAROS:  Q07020
GTEx:  ENSG00000063177 
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UniProt GroupQ07020
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aCA [auth LS]176Homo sapiensMutation(s): 0 
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Find proteins for Q02543 (Homo sapiens)
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GTEx:  ENSG00000105640 
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UniProt GroupQ02543
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21DA [auth LT]160Homo sapiensMutation(s): 0 
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Find proteins for P46778 (Homo sapiens)
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GTEx:  ENSG00000122026 
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UniProt GroupP46778
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23EA [auth LV]140Homo sapiensMutation(s): 0 
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Find proteins for P62829 (Homo sapiens)
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GTEx:  ENSG00000125691 
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UniProt GroupP62829
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26FA [auth LY]145Homo sapiensMutation(s): 0 
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Find proteins for P61254 (Homo sapiens)
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PHAROS:  P61254
GTEx:  ENSG00000161970 
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UniProt GroupP61254
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aGA [auth La]148Homo sapiensMutation(s): 0 
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Find proteins for P46776 (Homo sapiens)
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GTEx:  ENSG00000166441 
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UniProt GroupP46776
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31HA [auth Ld]125Homo sapiensMutation(s): 0 
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Find proteins for P62899 (Homo sapiens)
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GTEx:  ENSG00000071082 
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UniProt GroupP62899
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L32IA [auth Le]135Homo sapiensMutation(s): 0 
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Find proteins for P62910 (Homo sapiens)
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GTEx:  ENSG00000144713 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aJA [auth Lf]110Homo sapiensMutation(s): 0 
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Find proteins for P18077 (Homo sapiens)
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PHAROS:  P18077
GTEx:  ENSG00000182899 
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UniProt GroupP18077
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35KA [auth Lh]123Homo sapiensMutation(s): 0 
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Find proteins for P42766 (Homo sapiens)
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GTEx:  ENSG00000136942 
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UniProt GroupP42766
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36LA [auth Li]105Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3U8 (Homo sapiens)
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GTEx:  ENSG00000130255 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28MA [auth Lr]137Homo sapiensMutation(s): 0 
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Find proteins for P46779 (Homo sapiens)
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GTEx:  ENSG00000108107 
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UniProt GroupP46779
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11NA [auth Lt]165Homo sapiensMutation(s): 0 
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Find proteins for P30050 (Homo sapiens)
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GTEx:  ENSG00000197958 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aOA [auth Lz]217Homo sapiensMutation(s): 0 
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Find proteins for P62906 (Homo sapiens)
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GTEx:  ENSG00000198755 
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Reference Sequence
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Entity ID: 12
MoleculeChains LengthOrganismImage
28S rRNAL [auth L5]5,070Homo sapiens
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Entity ID: 13
MoleculeChains LengthOrganismImage
5S rRNAM [auth L7]121Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
5.8S rRNAN [auth L8]157Homo sapiens
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
PA [auth CB]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
SA [auth CD]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
TA [auth CI]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
QA [auth CB],
RA [auth CD]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release