8FLC

Human nuclear pre-60S ribosomal subunit (State K3)

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

  • Deposited: 2022-12-21 Released: 2023-07-12 
  • Deposition Author(s): Vanden Broeck, A., Klinge, S.
  • Funding Organization(s): European Molecular Biology Organization (EMBO), The G. Harold and Leila Y. Mathers Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Principles of human pre-60 S biogenesis.

Vanden Broeck, A.Klinge, S.

(2023) Science 381: eadh3892-eadh3892

  • DOI: https://doi.org/10.1126/science.adh3892
  • Primary Citation of Related Structures:  
    8FKP, 8FKQ, 8FKR, 8FKS, 8FKT, 8FKU, 8FKV, 8FKW, 8FKX, 8FKY, 8FKZ, 8FL0, 8FL2, 8FL3, 8FL4, 8FL6, 8FL7, 8FL9, 8FLA, 8FLB, 8FLC, 8FLD, 8FLE, 8FLF

  • PubMed Abstract: 

    During the early stages of human large ribosomal subunit (60 S ) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 S particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 S assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 S particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.


  • Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12A [auth BA]165Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P30050 (Homo sapiens)
Explore P30050 
Go to UniProtKB:  P30050
PHAROS:  P30050
GTEx:  ENSG00000197958 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30050
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11E [auth L5]178Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62913 (Homo sapiens)
Explore P62913 
Go to UniProtKB:  P62913
PHAROS:  P62913
GTEx:  ENSG00000142676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62913
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13F [auth L6]211Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P26373 (Homo sapiens)
Explore P26373 
Go to UniProtKB:  P26373
PHAROS:  P26373
GTEx:  ENSG00000167526 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26373
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aG [auth L7]203Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P40429 (Homo sapiens)
Explore P40429 
Go to UniProtKB:  P40429
PHAROS:  P40429
GTEx:  ENSG00000142541 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40429
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14H [auth L8]215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P50914 (Homo sapiens)
Explore P50914 
Go to UniProtKB:  P50914
PHAROS:  P50914
GTEx:  ENSG00000188846 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50914
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15I [auth L9]204Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61313 (Homo sapiens)
Explore P61313 
Go to UniProtKB:  P61313
PHAROS:  P61313
GTEx:  ENSG00000174748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61313
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17J [auth LA]184Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18621 (Homo sapiens)
Explore P18621 
Go to UniProtKB:  P18621
PHAROS:  P18621
GTEx:  ENSG00000265681 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18621
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18K [auth LB]188Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07020 (Homo sapiens)
Explore Q07020 
Go to UniProtKB:  Q07020
PHAROS:  Q07020
GTEx:  ENSG00000063177 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07020
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aL [auth LC]176Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q02543 (Homo sapiens)
Explore Q02543 
Go to UniProtKB:  Q02543
GTEx:  ENSG00000105640 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02543
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19M [auth LD]196Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P84098 (Homo sapiens)
Explore P84098 
Go to UniProtKB:  P84098
PHAROS:  P84098
GTEx:  ENSG00000108298 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84098
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21N [auth LE]160Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46778 (Homo sapiens)
Explore P46778 
Go to UniProtKB:  P46778
PHAROS:  P46778
GTEx:  ENSG00000122026 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46778
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22O [auth LF]128Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P35268 (Homo sapiens)
Explore P35268 
Go to UniProtKB:  P35268
PHAROS:  P35268
GTEx:  ENSG00000116251 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35268
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23P [auth LG]140Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62829 (Homo sapiens)
Explore P62829 
Go to UniProtKB:  P62829
PHAROS:  P62829
GTEx:  ENSG00000125691 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62829
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aQ [auth LH]156Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62750 (Homo sapiens)
Explore P62750 
Go to UniProtKB:  P62750
PHAROS:  P62750
GTEx:  ENSG00000198242 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62750
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26R [auth LI]145Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61254 (Homo sapiens)
Explore P61254 
Go to UniProtKB:  P61254
PHAROS:  P61254
GTEx:  ENSG00000161970 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61254
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27S [auth LJ]136Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61353 (Homo sapiens)
Explore P61353 
Go to UniProtKB:  P61353
PHAROS:  P61353
GTEx:  ENSG00000131469 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61353
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aT [auth LK]148Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46776 (Homo sapiens)
Explore P46776 
Go to UniProtKB:  P46776
PHAROS:  P46776
GTEx:  ENSG00000166441 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46776
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28U [auth LL]137Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46779 (Homo sapiens)
Explore P46779 
Go to UniProtKB:  P46779
PHAROS:  P46779
GTEx:  ENSG00000108107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46779
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29V [auth LM]159Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P47914 (Homo sapiens)
Explore P47914 
Go to UniProtKB:  P47914
GTEx:  ENSG00000162244 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47914
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3W [auth LN]403Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P39023 (Homo sapiens)
Explore P39023 
Go to UniProtKB:  P39023
PHAROS:  P39023
GTEx:  ENSG00000100316 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39023
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30X [auth LO]115Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62888 (Homo sapiens)
Explore P62888 
Go to UniProtKB:  P62888
PHAROS:  P62888
GTEx:  ENSG00000156482 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62888
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31Y [auth LP]125Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62899 (Homo sapiens)
Explore P62899 
Go to UniProtKB:  P62899
PHAROS:  P62899
GTEx:  ENSG00000071082 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32Z [auth LQ]135Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62910 (Homo sapiens)
Explore P62910 
Go to UniProtKB:  P62910
PHAROS:  P62910
GTEx:  ENSG00000144713 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62910
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34AA [auth LR]117Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P49207 (Homo sapiens)
Explore P49207 
Go to UniProtKB:  P49207
PHAROS:  P49207
GTEx:  ENSG00000109475 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49207
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35BA [auth LS]123Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P42766 (Homo sapiens)
Explore P42766 
Go to UniProtKB:  P42766
PHAROS:  P42766
GTEx:  ENSG00000136942 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42766
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aCA [auth LT]110Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18077 (Homo sapiens)
Explore P18077 
Go to UniProtKB:  P18077
PHAROS:  P18077
GTEx:  ENSG00000182899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18077
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36DA [auth LU]105Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3U8 (Homo sapiens)
Explore Q9Y3U8 
Go to UniProtKB:  Q9Y3U8
PHAROS:  Q9Y3U8
GTEx:  ENSG00000130255 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3U8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aEA [auth LV]106Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P83881 (Homo sapiens)
Explore P83881 
Go to UniProtKB:  P83881
PHAROS:  P83881
GTEx:  ENSG00000241343 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83881
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37FA [auth LW]97Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61927 (Homo sapiens)
Explore P61927 
Go to UniProtKB:  P61927
PHAROS:  P61927
GTEx:  ENSG00000145592 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61927
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aGA [auth LX]92Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61513 (Homo sapiens)
Explore P61513 
Go to UniProtKB:  P61513
PHAROS:  P61513
GTEx:  ENSG00000197756 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61513
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38HA [auth LY]70Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63173 (Homo sapiens)
Explore P63173 
Go to UniProtKB:  P63173
PHAROS:  P63173
GTEx:  ENSG00000172809 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63173
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39IA [auth LZ]51Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62891 (Homo sapiens)
Explore P62891 
Go to UniProtKB:  P62891
GTEx:  ENSG00000198918 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62891
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologJA [auth NK]129Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRT6 (Homo sapiens)
Explore Q9BRT6 
Go to UniProtKB:  Q9BRT6
PHAROS:  Q9BRT6
GTEx:  ENSG00000139233 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRT6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 593KA [auth NP]134Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O00488 (Homo sapiens)
Explore O00488 
Go to UniProtKB:  O00488
PHAROS:  O00488
GTEx:  ENSG00000142684 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00488
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Translation machinery-associated protein 16LA [auth NR]203Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY4 (Homo sapiens)
Explore Q96EY4 
Go to UniProtKB:  Q96EY4
PHAROS:  Q96EY4
GTEx:  ENSG00000198498 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EY4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4MA [auth SA]427Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P36578 (Homo sapiens)
Explore P36578 
Go to UniProtKB:  P36578
PHAROS:  P36578
GTEx:  ENSG00000174444 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36578
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5NA [auth SB]297Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46777 (Homo sapiens)
Explore P46777 
Go to UniProtKB:  P46777
PHAROS:  P46777
GTEx:  ENSG00000122406 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46777
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6OA [auth SC]288Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q02878 (Homo sapiens)
Explore Q02878 
Go to UniProtKB:  Q02878
PHAROS:  Q02878
GTEx:  ENSG00000089009 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02878
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7PA [auth SD]248Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18124 (Homo sapiens)
Explore P18124 
Go to UniProtKB:  P18124
PHAROS:  P18124
GTEx:  ENSG00000147604 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18124
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aQA [auth SE]266Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62424 (Homo sapiens)
Explore P62424 
Go to UniProtKB:  P62424
PHAROS:  P62424
GTEx:  ENSG00000148303 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62424
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8RA [auth SF]257Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62917 (Homo sapiens)
Explore P62917 
Go to UniProtKB:  P62917
GTEx:  ENSG00000161016 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62917
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9SA [auth SG]192Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P32969 (Homo sapiens)
Explore P32969 
Go to UniProtKB:  P32969
PHAROS:  P32969
GTEx:  ENSG00000163682 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32969
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6TA [auth SK]245Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P56537 (Homo sapiens)
Explore P56537 
Go to UniProtKB:  P56537
PHAROS:  P56537
GTEx:  ENSG00000242372 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56537
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologUA [auth SQ]239Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKD2 (Homo sapiens)
Explore Q9UKD2 
Go to UniProtKB:  Q9UKD2
PHAROS:  Q9UKD2
GTEx:  ENSG00000053372 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKD2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4VA [auth SR]634Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZE4 (Homo sapiens)
Explore Q9BZE4 
Go to UniProtKB:  Q9BZE4
PHAROS:  Q9BZE4
GTEx:  ENSG00000107937 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZE4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24WA [auth SV]163Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHA3 (Homo sapiens)
Explore Q9UHA3 
Go to UniProtKB:  Q9UHA3
PHAROS:  Q9UHA3
GTEx:  ENSG00000137876 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHA3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Leydig cell tumor 10 kDa protein homologXA [auth VB]99Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNZ5 (Homo sapiens)
Explore Q9UNZ5 
Go to UniProtKB:  Q9UNZ5
PHAROS:  Q9UNZ5
GTEx:  ENSG00000104979 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNZ5
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNAB [auth L1]157Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
28S rRNAC [auth L3]5,070Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth L4]121Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
ME [auth SR]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EE [auth LR]
GE [auth LV]
HE [auth LW]
JE [auth LX]
KE [auth NP]
EE [auth LR],
GE [auth LV],
HE [auth LW],
JE [auth LX],
KE [auth NP],
PE [auth SV]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
NE [auth SR]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth L1]
AC [auth L3]
AD [auth L3]
AE [auth LG]
BB [auth L3]
AB [auth L1],
AC [auth L3],
AD [auth L3],
AE [auth LG],
BB [auth L3],
BC [auth L3],
BD [auth L3],
BE [auth LN],
CB [auth L3],
CC [auth L3],
CD [auth L3],
CE [auth LQ],
DB [auth L3],
DC [auth L3],
DD [auth L3],
DE [auth LR],
EB [auth L3],
EC [auth L3],
ED [auth L3],
FB [auth L3],
FC [auth L3],
FD [auth L3],
FE [auth LT],
GB [auth L3],
GC [auth L3],
GD [auth L3],
HB [auth L3],
HC [auth L3],
HD [auth L3],
IB [auth L3],
IC [auth L3],
ID [auth L3],
IE [auth LW],
JB [auth L3],
JC [auth L3],
JD [auth L3],
KB [auth L3],
KC [auth L3],
KD [auth L3],
LB [auth L3],
LC [auth L3],
LD [auth L3],
LE [auth SF],
MB [auth L3],
MC [auth L3],
MD [auth L3],
NB [auth L3],
NC [auth L3],
ND [auth L3],
OB [auth L3],
OC [auth L3],
OD [auth L3],
OE [auth SR],
PB [auth L3],
PC [auth L3],
PD [auth L3],
QB [auth L3],
QC [auth L3],
QD [auth L3],
RB [auth L3],
RC [auth L3],
RD [auth L3],
SB [auth L3],
SC [auth L3],
SD [auth L3],
TB [auth L3],
TC [auth L3],
TD [auth L3],
UB [auth L3],
UC [auth L3],
UD [auth L3],
VB [auth L3],
VC [auth L3],
VD [auth L3],
WB [auth L3],
WC [auth L3],
WD [auth L3],
XB [auth L3],
XC [auth L3],
XD [auth L4],
YA [auth L1],
YB [auth L3],
YC [auth L3],
YD [auth L4],
ZA [auth L1],
ZB [auth L3],
ZC [auth L3],
ZD [auth L4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
W [auth LN]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
PTR
Query on PTR
LA [auth NR]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European UnionALTF 711-2019
The G. Harold and Leila Y. Mathers FoundationUnited StatesMF-2104-01554

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2023-07-26
    Changes: Database references