8FKW

Human nucleolar pre-60S ribosomal subunit (State D2)

  • 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: 2.50 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12A [auth BA]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aB [auth BB]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13F [auth L6]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aG [auth L7]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14H [auth L8]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15I [auth L9]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17J [auth LA]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18K [auth LB]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aL [auth LC]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21M [auth LE]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23N [auth LG]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aO [auth LH]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26P [auth LI]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aQ [auth LK]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28R [auth LL]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3S [auth LN]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31T [auth LP]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32U [auth LQ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35V [auth LS]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aW [auth LT]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36X [auth LU]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37Y [auth LW]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 2 homologZ [auth NA]749Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188976 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein-like 3AA [auth NB]549Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163938 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2 homologBA [auth NF]260Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164346 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosome subunit biogenesis protein NIP7 homologCA [auth NH]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132603 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX54DA [auth NI]881Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000123064 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologEA [auth NK]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139233 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4FA [auth SA]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6GA [auth SC]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7HA [auth SD]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aIA [auth SE]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9JA [auth SG]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
MKI67 FHA domain-interacting nucleolar phosphoproteinKA [auth SH]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000155438 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-like 1LA [auth SI]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000146223 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3MA [auth SJ]847Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000108592 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6NA [auth SK]245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242372 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L1 domain-containing protein 1OA [auth SL]490Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171490 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologPA [auth SM]588Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100029 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Probable rRNA-processing protein EBP2QA [auth SN]306Homo sapiensMutation(s): 0 
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Find proteins for Q99848 (Homo sapiens)
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PHAROS:  Q99848
GTEx:  ENSG00000117395 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BRX1 homologRA [auth SO]353Homo sapiensMutation(s): 0 
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Find proteins for Q8TDN6 (Homo sapiens)
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PHAROS:  Q8TDN6
GTEx:  ENSG00000113460 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologSA [auth SQ]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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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4TA [auth SR]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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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BOP1UA [auth SS]746Homo sapiensMutation(s): 0 
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Find proteins for Q14137 (Homo sapiens)
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GTEx:  ENSG00000261236 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis regulatory protein homologVA [auth ST]365Homo sapiensMutation(s): 0 
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Find proteins for Q15050 (Homo sapiens)
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GTEx:  ENSG00000179041 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 3 homologWA [auth SU]800Homo sapiensMutation(s): 0 
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Find proteins for Q8WTT2 (Homo sapiens)
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GTEx:  ENSG00000173145 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24XA [auth SV]163Homo sapiensMutation(s): 0 
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Find proteins for Q9UHA3 (Homo sapiens)
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GTEx:  ENSG00000137876 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX18YA [auth SW]670Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for Q9NVP1 (Homo sapiens)
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GTEx:  ENSG00000088205 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferaseZA [auth SY]812Homo sapiensMutation(s): 0 
EC: 2.1.1
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Find proteins for P46087 (Homo sapiens)
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GTEx:  ENSG00000111641 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 16AB [auth SZ]178Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3C1 (Homo sapiens)
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GTEx:  ENSG00000048162 
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNAC [auth L1]157Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
ITS2 rRNAD [auth L2]1,167Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
28S rRNAE [auth L3]5,070Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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ID [auth SR]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP
Query on ADP

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FD [auth NI]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

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ED [auth LW],
MD [auth SV]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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JD [auth SR]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth L3]
AD [auth L3]
BB [auth L1]
BC [auth L3]
BD [auth L9]
AC [auth L3],
AD [auth L3],
BB [auth L1],
BC [auth L3],
BD [auth L9],
CB [auth L1],
CC [auth L3],
CD [auth LQ],
DB [auth L1],
DC [auth L3],
DD [auth LT],
EB [auth L1],
EC [auth L3],
FB [auth L1],
FC [auth L3],
GB [auth L2],
GC [auth L3],
GD [auth NI],
HB [auth L3],
HC [auth L3],
HD [auth SA],
IB [auth L3],
IC [auth L3],
JB [auth L3],
JC [auth L3],
KB [auth L3],
KC [auth L3],
KD [auth SR],
LB [auth L3],
LC [auth L3],
LD [auth SU],
MB [auth L3],
MC [auth L3],
NB [auth L3],
NC [auth L3],
OB [auth L3],
OC [auth L3],
PB [auth L3],
PC [auth L3],
QB [auth L3],
QC [auth L3],
RB [auth L3],
RC [auth L3],
SB [auth L3],
SC [auth L3],
TB [auth L3],
TC [auth L3],
UB [auth L3],
UC [auth L3],
VB [auth L3],
VC [auth L3],
WB [auth L3],
WC [auth L3],
XB [auth L3],
XC [auth L3],
YB [auth L3],
YC [auth L3],
ZB [auth L3],
ZC [auth L3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
S [auth LN]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
SEP
Query on SEP
UA [auth SS]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.19.1

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: 2023-08-16
    Changes: Data collection