8FL2

Human nuclear pre-60S ribosomal subunit (State I1)

  • 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: 2.67 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 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal biogenesis protein LAS1LC [auth BD]734Homo sapiensMutation(s): 0 
EC: 3.1
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GTEx:  ENSG00000001497 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11H [auth L5]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13I [auth L6]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aJ [auth L7]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14K [auth L8]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15L [auth L9]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17M [auth LA]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18N [auth LB]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aO [auth LC]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19P [auth LD]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21Q [auth LE]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22R [auth LF]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23S [auth LG]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aT [auth LH]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26U [auth LI]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27V [auth LJ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aW [auth LK]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28X [auth LL]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3Y [auth LN]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30Z [auth LO]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31AA [auth LP]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32BA [auth LQ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34CA [auth LR]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35DA [auth LS]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aEA [auth LT]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36FA [auth LU]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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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
Guanine nucleotide-binding protein-like 3KA [auth NB]549Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163938 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2LA [auth NC]731Homo sapiensMutation(s): 0 
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PHAROS:  Q13823
GTEx:  ENSG00000134697 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2 homologMA [auth NF]260Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164346 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Notchless protein homolog 1NA [auth NJ]485Homo sapiensMutation(s): 0 
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Find proteins for Q9NVX2 (Homo sapiens)
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GTEx:  ENSG00000073536 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologOA [auth NK]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139233 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NOP53PA [auth NL]478Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105373 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 593QA [auth NP]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142684 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SDA1 homologRA [auth NT]687Homo sapiensMutation(s): 0 
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Find proteins for Q9NVU7 (Homo sapiens)
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PHAROS:  Q9NVU7
GTEx:  ENSG00000198301 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Testis-expressed protein 10SA [auth NU]929Homo sapiensMutation(s): 0 
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PHAROS:  Q9NXF1
GTEx:  ENSG00000136891 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 18TA [auth NV],
UA [auth NW]
432Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000065268 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Proline-, glutamic acid- and leucine-rich protein 1VA [auth NX],
WA [auth NY]
1,130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141456 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 86XA [auth NZ]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110104 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4YA [auth SA]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: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5ZA [auth SB]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6AB [auth SC]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7BB [auth SD]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aCB [auth SE]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8DB [auth SF]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9EB [auth SG]192Homo sapiensMutation(s): 0 
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Find proteins for P32969 (Homo sapiens)
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GTEx:  ENSG00000163682 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
MKI67 FHA domain-interacting nucleolar phosphoproteinFB [auth SH]293Homo sapiensMutation(s): 0 
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Find proteins for Q9BYG3 (Homo sapiens)
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GTEx:  ENSG00000155438 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-like 1GB [auth SI]255Homo sapiensMutation(s): 0 
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Find proteins for Q6DKI1 (Homo sapiens)
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GTEx:  ENSG00000146223 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6HB [auth SK]245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242372 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L1 domain-containing protein 1IB [auth SL]490Homo sapiensMutation(s): 0 
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Find proteins for O76021 (Homo sapiens)
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GTEx:  ENSG00000171490 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologJB [auth SM]588Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100029 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologKB [auth SQ]239Homo sapiensMutation(s): 0 
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Find proteins for Q9UKD2 (Homo sapiens)
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GTEx:  ENSG00000053372 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4LB [auth SR]634Homo sapiensMutation(s): 0 
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Find proteins for Q9BZE4 (Homo sapiens)
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GTEx:  ENSG00000107937 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24MB [auth SV]163Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137876 
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth L1]157Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
ITS2 rRNAE [auth L2]1,167Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
28S rRNAF [auth L3]5,070Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S rRNAG [auth L4]121Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
IF [auth NC]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

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

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DF [auth LR],
FF [auth LW],
HF [auth LX],
LF [auth NP],
RF [auth SV]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
KF [auth NC],
PF [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]
AF [auth L9]
BC [auth L3]
AC [auth L3],
AD [auth L3],
AE [auth L3],
AF [auth L9],
BC [auth L3],
BD [auth L3],
BE [auth L3],
BF [auth LQ],
CC [auth L3],
CD [auth L3],
CE [auth L3],
CF [auth LR],
DC [auth L3],
DD [auth L3],
DE [auth L3],
EC [auth L3],
ED [auth L3],
EE [auth L3],
EF [auth LT],
FC [auth L3],
FD [auth L3],
FE [auth L3],
GC [auth L3],
GD [auth L3],
GE [auth L3],
GF [auth LW],
HC [auth L3],
HD [auth L3],
HE [auth L3],
IC [auth L3],
ID [auth L3],
IE [auth L3],
JC [auth L3],
JD [auth L3],
JE [auth L3],
JF [auth NC],
KC [auth L3],
KD [auth L3],
KE [auth L3],
LC [auth L3],
LD [auth L3],
LE [auth L3],
MC [auth L3],
MD [auth L3],
ME [auth L3],
MF [auth SA],
NB [auth L1],
NC [auth L3],
ND [auth L3],
NE [auth L3],
NF [auth SF],
OB [auth L1],
OC [auth L3],
OD [auth L3],
OE [auth L3],
PB [auth L1],
PC [auth L3],
PD [auth L3],
PE [auth L3],
QB [auth L1],
QC [auth L3],
QD [auth L3],
QE [auth L3],
QF [auth SR],
RB [auth L1],
RC [auth L3],
RD [auth L3],
RE [auth L3],
SB [auth L3],
SC [auth L3],
SD [auth L3],
SE [auth L3],
TB [auth L3],
TC [auth L3],
TD [auth L3],
TE [auth L3],
UB [auth L3],
UC [auth L3],
UD [auth L3],
UE [auth L3],
VB [auth L3],
VC [auth L3],
VD [auth L3],
VE [auth L3],
WB [auth L3],
WC [auth L3],
WD [auth L3],
WE [auth L3],
XB [auth L3],
XC [auth L3],
XD [auth L3],
XE [auth L3],
YB [auth L3],
YC [auth L3],
YD [auth L3],
YE [auth L4],
ZB [auth L3],
ZC [auth L3],
ZD [auth L3],
ZE [auth L6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
Y [auth LN]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.19.1

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