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:  
    6CB1, 6C0F

  • 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 o ...

    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 NSA1A463Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 5
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60S ribosomal protein L4-AC362Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 6
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Protein MAK16D306Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
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60S ribosomal protein L6-AE176Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
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60S ribosomal protein L7-AF244Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
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60S ribosomal protein L8-AG256Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 10
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Ribosome production factor 1I295Saccharomyces 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-AS172Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L25X142Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L26-AY127Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L27-AZ136Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 22
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Nucleolar protein 167231Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 23
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Ribosome biogenesis protein BRX1b291Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L30c105Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 25
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Ribosome biogenesis protein YTM1d465Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 26
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60S ribosomal protein L32e130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L33-Af107Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 28
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60S ribosomal protein L34-Ag121Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 29
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60S ribosomal protein L35-Ah120Saccharomyces cerevisiae BY4741Mutation(s): 0 
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60S ribosomal protein L36-Ai100Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 31
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60S ribosomal protein L37-Aj88Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 32
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60S ribosomal protein L38k78Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 33
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rRNA-processing protein EBP2m102Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 34
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Pescadillo homologn605Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 35
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Ribosome biogenesis protein 15o220Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 36
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ATP-dependent RNA helicase HAS1p505Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3.6.4.13
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1s569Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for A6ZMA9 (Saccharomyces cerevisiae (strain YJM789))
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Find proteins for Q04660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7t322Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 39
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BRX1 associated peptidex28Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1z278Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
35S pre-ribosomal RNA miscRNA13396Saccharomyces cerevisiae BY4741
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5.8S rRNA2158Saccharomyces cerevisiae BY4741
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Entity ID: 3
MoleculeChainsLengthOrganismImage
ITS26232Saccharomyces cerevisiae BY4741
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D, 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 

  • 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