6CB1

Yeast nucleolar pre-60S ribosomal subunit (state 3)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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

Modular assembly of the nucleolar pre-60S ribosomal subunit.

Sanghai, Z.A., Miller, L., Molloy, K.R., Barandun, J., Hunziker, M., Chaker-Margot, M., Wang, J., Chait, B.T., Klinge, S.

(2018) Nature 556: 126-129

  • DOI: 10.1038/nature26156
  • Primary Citation of Related Structures:  
    6C0F, 6CB1

  • PubMed Abstract: 

    • Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains ...

    Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.

    Organizational Affiliation: 

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA1D [auth A]463Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 5
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60S ribosomal protein L4-AE [auth C]362Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 6
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Protein MAK16F [auth D]306Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 7
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60S ribosomal protein L6-AG [auth E]176Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AH [auth F]244Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 9
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60S ribosomal protein L8-AI [auth G]256Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 10
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Ribosome production factor 1J [auth I]295Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 11
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Proteasome-interacting protein CIC1K376Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L13-AL199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L14-AM138Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 14
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60S ribosomal protein L15-AN204Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L16-AO199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L17-AP184Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 17
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60S ribosomal protein L18-AQ186Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L20-AR [auth S]172Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L25S [auth X]142Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L26-AT [auth Y]127Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L27-AU [auth Z]136Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 22
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Nucleolar protein 16V [auth 7]231Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 23
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Ribosome biogenesis protein BRX1W [auth b]291Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L30X [auth c]105Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Ribosome biogenesis protein YTM1Y [auth d]465Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 26
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60S ribosomal protein L32Z [auth e]130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L33-AAA [auth f]107Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 28
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60S ribosomal protein L34-ABA [auth g]121Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L35-ACA [auth h]120Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L36-ADA [auth i]100Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 31
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60S ribosomal protein L37-AEA [auth j]88Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 32
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60S ribosomal protein L38FA [auth k]78Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 33
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rRNA-processing protein EBP2GA [auth m]102Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 34
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Pescadillo homologHA [auth n]605Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 35
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Ribosome biogenesis protein 15IA [auth o]220Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HAS1JA [auth p]505Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3.6.4.13
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Entity ID: 37
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Ribosome biogenesis protein ERB1KA [auth s]569Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Find proteins for A6ZMA9 (Saccharomyces cerevisiae (strain YJM789))
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Entity ID: 38
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Ribosome biogenesis protein RLP7LA [auth t]322Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 39
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BRX1 associated peptideMA [auth x]28Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 40
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Ribosomal RNA-processing protein 1NA [auth z]278Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
35S pre-ribosomal RNA miscRNAA [auth 1]3396Saccharomyces cerevisiae BY4741
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5.8S rRNAB [auth 2]158Saccharomyces cerevisiae BY4741
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Entity ID: 3
MoleculeChainsLengthOrganismImage
ITS2C [auth 6]232Saccharomyces cerevisiae BY4741
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
OA [auth D], PA [auth j]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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 States1DP2GM123459
Swiss National Science FoundationSwitzerland155515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115327-Tan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103314
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM109824

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence