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:  
    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA1A463Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P53136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53136 
Go to UniProtKB:  P53136
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3B387Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14126 
Go to UniProtKB:  P14126
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AC362Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10664 
Go to UniProtKB:  P10664
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Protein MAK16D306Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10962 
Go to UniProtKB:  P10962
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AE176Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02326 
Go to UniProtKB:  Q02326
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AF244Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05737 
Go to UniProtKB:  P05737
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-AG256Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17076 
Go to UniProtKB:  P17076
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome production factor 1I295Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P38805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38805 
Go to UniProtKB:  P38805
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome-interacting protein CIC1K376Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38779 
Go to UniProtKB:  P38779
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13-AL199Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12690 
Go to UniProtKB:  Q12690
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AM138Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36105 
Go to UniProtKB:  P36105
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AN204Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05748 
Go to UniProtKB:  P05748
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-AO199Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26784 
Go to UniProtKB:  P26784
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-AP184Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05740 
Go to UniProtKB:  P05740
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-AQ186Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX49 
Go to UniProtKB:  P0CX49
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-AS172Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX23 
Go to UniProtKB:  P0CX23
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23-AV137Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX41 
Go to UniProtKB:  P0CX41
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1W647Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02892 
Go to UniProtKB:  Q02892
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-AY127Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05743 
Go to UniProtKB:  P05743
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar protein 167231Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P40007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40007 
Go to UniProtKB:  P40007
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 148434Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P36080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36080 
Go to UniProtKB:  P36080
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein BRX1b291Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q08235 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08235 
Go to UniProtKB:  Q08235
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32e130Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38061 
Go to UniProtKB:  P38061
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-Af107Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05744 
Go to UniProtKB:  P05744
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-Ah120Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX84 
Go to UniProtKB:  P0CX84
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-Ai100Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05745 
Go to UniProtKB:  P05745
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-Aj88Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49166 
Go to UniProtKB:  P49166
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Brx1-associated peptidex28Saccharomyces cerevisiae BY4741Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA-processing protein EBP2m74Saccharomyces cerevisiae BY4741Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pescadillo homologn605Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53261 
Go to UniProtKB:  P53261
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein 15o220Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53927 
Go to UniProtKB:  P53927
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HAS1p505Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 3.6.4.13
Find proteins for Q03532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03532 
Go to UniProtKB:  Q03532
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Protein MAK11q285Saccharomyces cerevisiae BY4741Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1s807Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q04660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04660 
Go to UniProtKB:  Q04660
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7t322Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40693 
Go to UniProtKB:  P40693
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24u199Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07915 
Go to UniProtKB:  Q07915
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein SSF1v453Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P38789 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38789 
Go to UniProtKB:  P38789
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 15w250Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q06511 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06511 
Go to UniProtKB:  Q06511
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6y245Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12522 
Go to UniProtKB:  Q12522
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1z278Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35178 
Go to UniProtKB:  P35178
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA13395Saccharomyces cerevisiae BY4741
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5.8S rRNA2158Saccharomyces cerevisiae BY4741
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
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, 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

View Full Validation Report



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