9QJC | pdb_00009qjc

Yeast pre-60S Domain II intermediate

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

A comprehensive view on r- protein binding and rRNA domain structuring during early ribosome formation

Gerhalter, M., Prattes, M., Grundmann, L., Grishkovskaya, I., Semarari, E.F., Zisser, G., Harald, K., Merl-Pharm, J., Hauck, S.M., Haselbach, D., Bergler, H.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein MAK21A [auth 5]1,025Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12176 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 2B [auth 6]710Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NOC2, YOR206W, YOX001
UniProt
Find proteins for P39744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-A362Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MAK16306Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MAK16, YAL025C
UniProt
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-A176Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-A244Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AG [auth M]138Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AH [auth O]199Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AI [auth Q]186Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AJ [auth S]172Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32K [auth e]130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AL [auth f]107Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1M [auth z]278Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP1, YDR087C, D4478
UniProt
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 4P [auth B]685Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NOP4, NOP77, YPL043W
UniProt
Find proteins for P37838 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChains LengthOrganismImage
25S ribosomal RNAN [auth 1]3,396Saccharomyces cerevisiae
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Entity ID: 15
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAO [auth 2]159Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC3.0 - 4.6

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Austrian Science FundAustriaPAT1908524

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release