8FLA

Human nuclear pre-60S ribosomal subunit (State K1)

  • 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: 2.63 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11F [auth L5]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13G [auth L6]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aH [auth L7]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14I [auth L8]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15J [auth L9]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17K [auth LA]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18L [auth LB]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aM [auth LC]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19N [auth LD]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21O [auth LE]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22P [auth LF]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23Q [auth LG]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aR [auth LH]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26S [auth LI]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27T [auth LJ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aU [auth LK]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28V [auth LL]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29W [auth LM]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3X [auth LN]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30Y [auth LO]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31Z [auth LP]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32AA [auth LQ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34BA [auth LR]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35CA [auth LS]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aDA [auth LT]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36EA [auth LU]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aFA [auth LV]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37GA [auth LW]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aHA [auth LX]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38IA [auth LY]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39JA [auth LZ]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologKA [auth NK]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139233 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NOP53LA [auth NL]478Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105373 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 593MA [auth NP]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142684 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Translation machinery-associated protein 16NA [auth NR]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198498 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4OA [auth SA]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5PA [auth SB]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6QA [auth SC]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7RA [auth SD]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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UniProt GroupP18124
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aSA [auth SE]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8TA [auth SF]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9UA [auth SG]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
MKI67 FHA domain-interacting nucleolar phosphoproteinVA [auth SH]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000155438 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-like 1WA [auth SI]255Homo sapiensMutation(s): 0 
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PHAROS:  Q6DKI1
GTEx:  ENSG00000146223 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6XA [auth SK]245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242372 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L1 domain-containing protein 1YA [auth SL]490Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171490 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologZA [auth SM]588Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100029 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologAB [auth SQ]239Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000053372 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4BB [auth SR]634Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107937 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24CB [auth SV]163Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137876 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Leydig cell tumor 10 kDa protein homologDB [auth VB]99Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104979 
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNAB [auth L1]157Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
ITS2 rRNAC [auth L2]1,167Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
28S rRNAD [auth L3]5,070Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAE [auth L4]121Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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JE [auth LR]
LE [auth LV]
ME [auth LW]
OE [auth LX]
PE [auth NP]
JE [auth LR],
LE [auth LV],
ME [auth LW],
OE [auth LX],
PE [auth NP],
VE [auth SV]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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

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AC [auth L3]
AD [auth L3]
AE [auth L3]
BC [auth L3]
BD [auth L3]
AC [auth L3],
AD [auth L3],
AE [auth L3],
BC [auth L3],
BD [auth L3],
BE [auth L3],
CC [auth L3],
CD [auth L3],
CE [auth L3],
DC [auth L3],
DD [auth L3],
DE [auth L4],
EB [auth L1],
EC [auth L3],
ED [auth L3],
EE [auth L4],
FB [auth L1],
FC [auth L3],
FD [auth L3],
FE [auth L4],
GB [auth L1],
GC [auth L3],
GD [auth L3],
GE [auth LG],
HB [auth L3],
HC [auth L3],
HD [auth L3],
HE [auth LN],
IB [auth L3],
IC [auth L3],
ID [auth L3],
IE [auth LQ],
JB [auth L3],
JC [auth L3],
JD [auth L3],
KB [auth L3],
KC [auth L3],
KD [auth L3],
KE [auth LT],
LB [auth L3],
LC [auth L3],
LD [auth L3],
MB [auth L3],
MC [auth L3],
MD [auth L3],
NB [auth L3],
NC [auth L3],
ND [auth L3],
NE [auth LW],
OB [auth L3],
OC [auth L3],
OD [auth L3],
PB [auth L3],
PC [auth L3],
PD [auth L3],
QB [auth L3],
QC [auth L3],
QD [auth L3],
QE [auth SA],
RB [auth L3],
RC [auth L3],
RD [auth L3],
RE [auth SF],
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],
UE [auth SR],
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 L3],
YB [auth L3],
YC [auth L3],
YD [auth L3],
ZB [auth L3],
ZC [auth L3],
ZD [auth L3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
X [auth LN]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
PTR
Query on PTR
NA [auth NR]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

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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