8FL3

Human nuclear pre-60S ribosomal subunit (State I2)

  • 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: 2.53 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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Find proteins for P30050 (Homo sapiens)
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PHAROS:  P30050
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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Find proteins for P62906 (Homo sapiens)
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PHAROS:  P62906
GTEx:  ENSG00000198755 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal biogenesis protein LAS1LC [auth BD]734Homo sapiensMutation(s): 0 
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PHAROS:  Q9Y4W2
GTEx:  ENSG00000001497 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11G [auth L5]178Homo sapiensMutation(s): 0 
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PHAROS:  P62913
GTEx:  ENSG00000142676 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13H [auth L6]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aI [auth L7]203Homo sapiensMutation(s): 0 
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PHAROS:  P40429
GTEx:  ENSG00000142541 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14J [auth L8]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15K [auth L9]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17L [auth LA]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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UniProt GroupP18621
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18M [auth LB]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aN [auth LC]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19O [auth LD]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21P [auth LE]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22Q [auth LF]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23R [auth LG]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aS [auth LH]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26T [auth LI]145Homo sapiensMutation(s): 0 
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PHAROS:  P61254
GTEx:  ENSG00000161970 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27U [auth LJ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aV [auth LK]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28W [auth LL]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3X [auth LN]403Homo sapiensMutation(s): 0 
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Find proteins for P39023 (Homo sapiens)
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PHAROS:  P39023
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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Find proteins for P49207 (Homo sapiens)
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PHAROS:  P49207
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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Find proteins for P42766 (Homo sapiens)
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PHAROS:  P42766
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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PHAROS:  P18077
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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Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS:  Q9Y3U8
GTEx:  ENSG00000130255 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37FA [auth LW]97Homo sapiensMutation(s): 0 
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PHAROS:  P61927
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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PHAROS:  P63173
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
Guanine nucleotide-binding protein-like 3JA [auth NB]549Homo sapiensMutation(s): 0 
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Find proteins for Q9BVP2 (Homo sapiens)
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PHAROS:  Q9BVP2
GTEx:  ENSG00000163938 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2KA [auth NC]731Homo sapiensMutation(s): 0 
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Find proteins for Q13823 (Homo sapiens)
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GTEx:  ENSG00000134697 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2 homologLA [auth NF]260Homo sapiensMutation(s): 0 
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Find proteins for O95478 (Homo sapiens)
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GTEx:  ENSG00000164346 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Notchless protein homolog 1MA [auth NJ]485Homo sapiensMutation(s): 0 
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Find proteins for Q9NVX2 (Homo sapiens)
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PHAROS:  Q9NVX2
GTEx:  ENSG00000073536 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologNA [auth NK]129Homo sapiensMutation(s): 0 
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PHAROS:  Q9BRT6
GTEx:  ENSG00000139233 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NOP53OA [auth NL]478Homo sapiensMutation(s): 0 
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Find proteins for Q9NZM5 (Homo sapiens)
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PHAROS:  Q9NZM5
GTEx:  ENSG00000105373 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 593PA [auth NP]134Homo sapiensMutation(s): 0 
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PHAROS:  O00488
GTEx:  ENSG00000142684 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SDA1 homologQA [auth NT]687Homo sapiensMutation(s): 0 
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PHAROS:  Q9NVU7
GTEx:  ENSG00000198301 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Testis-expressed protein 10RA [auth NU]929Homo sapiensMutation(s): 0 
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PHAROS:  Q9NXF1
GTEx:  ENSG00000136891 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 18SA [auth NV],
TA [auth NW]
432Homo sapiensMutation(s): 0 
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PHAROS:  Q9BV38
GTEx:  ENSG00000065268 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Proline-, glutamic acid- and leucine-rich protein 1UA [auth NX],
VA [auth NY]
1,130Homo sapiensMutation(s): 0 
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Find proteins for Q8IZL8 (Homo sapiens)
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PHAROS:  Q8IZL8
GTEx:  ENSG00000141456 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 86WA [auth NZ]360Homo sapiensMutation(s): 0 
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PHAROS:  Q9H6F5
GTEx:  ENSG00000110104 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4XA [auth SA]427Homo sapiensMutation(s): 0 
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PHAROS:  P36578
GTEx:  ENSG00000174444 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5YA [auth SB]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6ZA [auth SC]288Homo sapiensMutation(s): 0 
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PHAROS:  Q02878
GTEx:  ENSG00000089009 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7AB [auth SD]248Homo sapiensMutation(s): 0 
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PHAROS:  P18124
GTEx:  ENSG00000147604 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aBB [auth SE]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8CB [auth SF]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9DB [auth SG]192Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P32969 (Homo sapiens)
Go to UniProtKB:  P32969
PHAROS:  P32969
GTEx:  ENSG00000163682 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
MKI67 FHA domain-interacting nucleolar phosphoproteinEB [auth SH]293Homo sapiensMutation(s): 0 
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Find proteins for Q9BYG3 (Homo sapiens)
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PHAROS:  Q9BYG3
GTEx:  ENSG00000155438 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-like 1FB [auth SI]255Homo sapiensMutation(s): 0 
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Find proteins for Q6DKI1 (Homo sapiens)
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PHAROS:  Q6DKI1
GTEx:  ENSG00000146223 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6GB [auth SK]245Homo sapiensMutation(s): 0 
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Find proteins for P56537 (Homo sapiens)
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PHAROS:  P56537
GTEx:  ENSG00000242372 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologHB [auth SM]588Homo sapiensMutation(s): 0 
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Find proteins for O00541 (Homo sapiens)
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PHAROS:  O00541
GTEx:  ENSG00000100029 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologIB [auth SQ]239Homo sapiensMutation(s): 0 
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Find proteins for Q9UKD2 (Homo sapiens)
Go to UniProtKB:  Q9UKD2
PHAROS:  Q9UKD2
GTEx:  ENSG00000053372 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4JB [auth SR]634Homo sapiensMutation(s): 0 
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Find proteins for Q9BZE4 (Homo sapiens)
Explore Q9BZE4 
Go to UniProtKB:  Q9BZE4
PHAROS:  Q9BZE4
GTEx:  ENSG00000107937 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZE4
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24KB [auth SV]163Homo sapiensMutation(s): 0 
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Find proteins for Q9UHA3 (Homo sapiens)
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PHAROS:  Q9UHA3
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
28S rRNAE [auth L3]5,070Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
5S rRNAF [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 
GF [auth NC]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

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

Download Ideal Coordinates CCD File 
BF [auth LR],
DF [auth LW],
FF [auth LX],
JF [auth NP],
PF [auth SV]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
IF [auth NC],
NF [auth SR]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth L3]
AD [auth L3]
AE [auth L3]
AF [auth LR]
BC [auth L3]
AC [auth L3],
AD [auth L3],
AE [auth L3],
AF [auth LR],
BC [auth L3],
BD [auth L3],
BE [auth L3],
CC [auth L3],
CD [auth L3],
CE [auth L3],
CF [auth LT],
DC [auth L3],
DD [auth L3],
DE [auth L3],
EC [auth L3],
ED [auth L3],
EE [auth L3],
EF [auth LW],
FC [auth L3],
FD [auth L3],
FE [auth L3],
GC [auth L3],
GD [auth L3],
GE [auth L3],
HC [auth L3],
HD [auth L3],
HE [auth L3],
HF [auth NC],
IC [auth L3],
ID [auth L3],
IE [auth L3],
JC [auth L3],
JD [auth L3],
JE [auth L3],
KC [auth L3],
KD [auth L3],
KE [auth L3],
KF [auth SA],
LB [auth L1],
LC [auth L3],
LD [auth L3],
LE [auth L3],
LF [auth SF],
MB [auth L1],
MC [auth L3],
MD [auth L3],
ME [auth L3],
NB [auth L1],
NC [auth L3],
ND [auth L3],
NE [auth L3],
OB [auth L1],
OC [auth L3],
OD [auth L3],
OE [auth L3],
OF [auth SR],
PB [auth L3],
PC [auth L3],
PD [auth L3],
PE [auth L3],
QB [auth L3],
QC [auth L3],
QD [auth L3],
QE [auth L3],
RB [auth L3],
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 L4],
YB [auth L3],
YC [auth L3],
YD [auth L3],
YE [auth L9],
ZB [auth L3],
ZC [auth L3],
ZD [auth L3],
ZE [auth LQ]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
X [auth LN]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 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