6C0F

Yeast nucleolar pre-60S ribosomal subunit (state 2)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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 L3E [auth B]387Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AF [auth C]362Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Protein MAK16G [auth D]306Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AH [auth E]176Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AI [auth F]244Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-AJ [auth G]256Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome production factor 1K [auth I]295Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 12
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Proteasome-interacting protein CIC1L [auth K]376Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L13-AM [auth L]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AN [auth M]138Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AO [auth N]204Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-AP [auth O]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 17
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60S ribosomal protein L17-AQ [auth P]184Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-AR [auth Q]186Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L20-AS172Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L23-AT [auth V]137Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1U [auth W]647Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 22
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60S ribosomal protein L26-AV [auth Y]127Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 23
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Nucleolar protein 16W [auth 7]231Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 24
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Ribosomal RNA-processing protein 14X [auth 8]434Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 25
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Ribosome biogenesis protein BRX1Y [auth b]291Saccharomyces 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 L35-ABA [auth h]120Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 29
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60S ribosomal protein L36-ACA [auth i]100Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 30
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60S ribosomal protein L37-ADA [auth j]88Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 31
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Brx1-associated peptideEA [auth x]28Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 32
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rRNA-processing protein EBP2FA [auth m]74Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pescadillo homologGA [auth n]605Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein 15HA [auth o]220Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HAS1IA [auth p]505Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3.6.4.13
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Protein MAK11JA [auth q]285Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1KA [auth s]807Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q04660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
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Ribosome biogenesis protein RLP7LA [auth t]322Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24MA [auth u]199Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 40
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Ribosome biogenesis protein SSF1NA [auth v]453Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 41
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Ribosomal RNA-processing protein 15OA [auth w]250Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6PA [auth y]245Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 43
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Ribosomal RNA-processing protein 1QA [auth z]278Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNAA [auth 1]3395Saccharomyces 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 RA [auth D], SA [auth j], TA [auth u]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

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