8ETH

Ytm1 associated 60S nascent ribosome State 1B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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
Ribosomal RNA-processing protein 1 homologD [auth 4]217Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein nsa1E [auth 5]387Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein brx1G [auth A]295Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3-AH [auth B]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-BI [auth C]363Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase has1J [auth D]578Schizosaccharomyces pombeMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6K [auth E]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-BL [auth F]250Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8M [auth G]259Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AN [auth H]190Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Probable rRNA-processing protein ebp2O [auth J]333Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosome biogenesis protein C8F11.04P [auth K]373Schizosaccharomyces 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
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AS [auth N]201Schizosaccharomyces pombeMutation(s): 0 
UniProt
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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 L20-AW [auth S]176Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AX [auth V]139Schizosaccharomyces 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
Probable nucleolar GTP-binding protein 1Z [auth b]642Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-AAA [auth e]127Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-BBA [auth f]108Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35CA [auth h]122Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-BDA [auth i]99Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-BEA [auth j]91Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein erb1FA [auth m]740Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologGA [auth n]607Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized RNA-binding protein C1827.05cHA [auth o]276Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein nsa2IA [auth r]260Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AJA [auth t]249Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein rlp24KA [auth u]192Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 16LA [auth v]209Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Brix domain-containing protein C4F8.04MA [auth x]306Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6NA [auth y]244Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AOA [auth T]160Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (1263-MER)A [auth 1]3,497Schizosaccharomyces pombe
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (130-MER)B [auth 2]165Schizosaccharomyces pombe
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (75-MER)F [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 
PA [auth j]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 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