8FLF

Human nuclear pre-60S ribosomal subunit (State L3)

  • 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: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 L10A [auth BE]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147403 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11E [auth L5]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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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 L19M [auth LD]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21N [auth LE]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22O [auth LF]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23P [auth LG]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aQ [auth LH]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26R [auth LI]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27S [auth LJ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aT [auth LK]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28U [auth LL]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29V [auth LM]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3W [auth LN]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30X [auth LO]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31Y [auth LP]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32Z [auth LQ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34AA [auth LR]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35BA [auth LS]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aCA [auth LT]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36DA [auth LU]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aEA [auth LV]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37FA [auth LW]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aGA [auth LX]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38HA [auth LY]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39IA [auth LZ]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologJA [auth NK]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139233 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 593KA [auth NP]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142684 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4LA [auth SA]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5MA [auth SB]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6NA [auth SC]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7OA [auth SD]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aPA [auth SE]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8QA [auth SF]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9RA [auth SG]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: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6SA [auth SK]245Homo sapiensMutation(s): 0 
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PHAROS:  P56537
GTEx:  ENSG00000242372 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologTA [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: 47
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4UA [auth SR]634Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107937 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24VA [auth SV]163Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137876 
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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
28S rRNAC [auth L3]5,070Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth L4]121Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
AB [auth L1]
AC [auth L3]
AD [auth L3]
AE [auth LQ]
BB [auth L3]
AB [auth L1],
AC [auth L3],
AD [auth L3],
AE [auth LQ],
BB [auth L3],
BC [auth L3],
BD [auth L3],
CB [auth L3],
CC [auth L3],
CD [auth L3],
CE [auth LT],
DB [auth L3],
DC [auth L3],
DD [auth L3],
EB [auth L3],
EC [auth L3],
ED [auth L3],
FB [auth L3],
FC [auth L3],
FD [auth L3],
FE [auth LW],
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 SA],
JB [auth L3],
JC [auth L3],
JD [auth L3],
JE [auth SF],
KB [auth L3],
KC [auth L3],
KD [auth L3],
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],
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],
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 L4],
VB [auth L3],
VC [auth L3],
VD [auth L4],
WA [auth L1],
WB [auth L3],
WC [auth L3],
WD [auth L4],
XA [auth L1],
XB [auth L3],
XC [auth L3],
XD [auth LG],
YA [auth L1],
YB [auth L3],
YC [auth L3],
YD [auth LM],
ZA [auth L1],
ZB [auth L3],
ZC [auth L3],
ZD [auth LN]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
W [auth LN]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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: 2024-05-01
    Changes: Data collection, Database references