8ETG

Fkbp39 associated 60S nascent ribosome State 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Chromatin localization of nucleophosmin organizes ribosome biogenesis.

Ugolini, I.Bilokapic, S.Ferrolino, M.Teague, J.Yan, Y.Zhou, X.Deshmukh, A.White, M.Kriwacki, R.W.Halic, M.

(2022) Mol Cell 82: 4443

  • DOI: https://doi.org/10.1016/j.molcel.2022.10.033
  • Primary Citation of Related Structures:  
    8ESQ, 8ESR, 8ETC, 8ETG, 8ETH, 8ETI, 8ETJ, 8EUG, 8EUI, 8EUP, 8EUY, 8EV3

  • PubMed Abstract: 

    Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.


  • Organizational Affiliation

    Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mak16C [auth 3]302Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein brx1D [auth A]295Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3-AE [auth B]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-BF [auth C]363Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase has1G [auth D]578Schizosaccharomyces pombeMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q09916 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6H [auth E]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-BI [auth F]250Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8J [auth G]259Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AK [auth H]190Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosome biogenesis protein C8F11.04L [auth K]373Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13M [auth L]208Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74175 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14N [auth M]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AO [auth N]201Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-BP [auth O]197Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AQ [auth P]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AR [auth Q]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AS [auth R]193Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AT [auth S]176Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22117Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-A139Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor mrt4241Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25-A141Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26126Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-A136Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28-AAA [auth a]148Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Probable nucleolar GTP-binding protein 1BA [auth b]642Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30-2CA [auth c]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31DA [auth d]113Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-AEA [auth e]127Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-BFA [auth f]108Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AGA [auth g]112Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35HA [auth h]122Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-BIA [auth i]99Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-BJA [auth j]91Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38-1KA [auth k]74Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein erb1LA [auth m]740Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologMA [auth n]607Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized RNA-binding protein C1827.05cNA [auth o]276Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ytm1OA [auth p]440Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein nsa2PA [auth r]260Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AQA [auth t]249Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein rlp24RA [auth u]192Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 16SA [auth v]209Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6TA [auth y]244Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94476 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupO94476
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AUA [auth T]160Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9UUC1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UUC1 
Go to UniProtKB:  Q9UUC1
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UniProt GroupQ9UUC1
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (1912-MER)A [auth 1]3,497Schizosaccharomyces pombe
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (146-MER)B [auth 2]165Schizosaccharomyces pombe
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Entity ID: 48
MoleculeChains LengthOrganismImage
RNA (62-MER)VA [auth 6]300Schizosaccharomyces pombe
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
WA [auth j]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM141694
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM141694
German Research Foundation (DFG)GermanyCryoNucleosome
European Research Council (ERC)European UnionERC-smallRNAhet-309584

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references