8EUG

Ytm1 associated nascent 60S ribosome State 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
60S ribosomal protein L39D [auth 8]51Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AF [auth A]253Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3-AG [auth B]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P40372 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-BH [auth C]363Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P784 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5-AI [auth D]294Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P52822 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6J [auth E]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-BK [auth F]250Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P25457 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8L [auth G]259Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AM [auth H]190Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-AN [auth I]221Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q09127 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AO [auth J]174Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AP [auth K]94Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13Q [auth L]208Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14R [auth M]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94238 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AS [auth N]201Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74895 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-BT [auth O]197Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AU [auth P]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AV [auth Q]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AW [auth R]193Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AX [auth S]176Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AY [auth T]160Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9UUC1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22Z [auth U]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AAA [auth V]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT60 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25-ABA [auth X]141Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26CA [auth Y]126Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ADA [auth Z]136Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28-AEA [auth a]148Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29FA [auth b]61Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30-2GA [auth c]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9UTP0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31HA [auth d]113Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-AIA [auth e]127Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-BJA [auth f]108Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AKA [auth g]112Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35LA [auth h]122Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-BMA [auth i]99Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-BNA [auth j]91Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38-1OA [auth k]74Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein erb1PA [auth m]740Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologQA [auth n]607Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42RA [auth o]106Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ytm1SA [auth p]440Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein rlp24TA [auth u]192Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (2863-MER)A [auth 1]3,498Schizosaccharomyces pombe
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (152-MER)B [auth 2]165Schizosaccharomyces pombe
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Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (118-MER)E [auth 9]229Schizosaccharomyces pombe
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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 StatesGM135599
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
  • Version 1.3: 2024-06-19
    Changes: Data collection