5Z3G

Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 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

Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate.

Zhou, D.Zhu, X.Zheng, S.Tan, D.Dong, M.Q.Ye, K.

(2019) Protein Cell 10: 120-130

  • DOI: https://doi.org/10.1007/s13238-018-0526-7
  • Primary Citation of Related Structures:  
    5Z1G, 5Z3G

  • PubMed Abstract: 

    Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 Å resolution, revealing a half-assembled subunit. Domains I, II and VI of 25S/5.8S rRNA pack tightly into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.


  • Organizational Affiliation

    Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7322Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40693 
Go to UniProtKB:  P40693
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40693
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein 15220Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53927 
Go to UniProtKB:  P53927
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53927
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3387Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14126 
Go to UniProtKB:  P14126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14126
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-A362Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10664 
Go to UniProtKB:  P10664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10664
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome-interacting protein CIC1376Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38779 
Go to UniProtKB:  P38779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38779
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-A176Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02326 
Go to UniProtKB:  Q02326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02326
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-A244Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05737 
Go to UniProtKB:  P05737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05737
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-A256Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17076 
Go to UniProtKB:  P17076
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17076
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-A191Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05738 
Go to UniProtKB:  P05738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05738
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 7605Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53261 
Go to UniProtKB:  P53261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53261
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6245Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12522 
Go to UniProtKB:  Q12522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12522
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome production factor 1295Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38805 
Go to UniProtKB:  P38805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-A199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12690 
Go to UniProtKB:  Q12690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12690
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-A138Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36105 
Go to UniProtKB:  P36105
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36105
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-A204Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05748 
Go to UniProtKB:  P05748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05748
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-A199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26784 
Go to UniProtKB:  P26784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26784
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-A184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05740 
Go to UniProtKB:  P05740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05740
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-A186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX49 
Go to UniProtKB:  P0CX49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX49
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA1463Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53136 
Go to UniProtKB:  P53136
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53136
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-A172Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX23 
Go to UniProtKB:  P0CX23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX23
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1278Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35178 
Go to UniProtKB:  P35178
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35178
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HAS1505Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q03532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03532 
Go to UniProtKB:  Q03532
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03532
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MAK16306Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10962 
Go to UniProtKB:  P10962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10962
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BRX1AA [auth a]291Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08235 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08235 
Go to UniProtKB:  Q08235
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08235
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein EBP2BA [auth b]427Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36049 
Go to UniProtKB:  P36049
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36049
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ACA [auth c]127Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05743 
Go to UniProtKB:  P05743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
UnassignedDA [auth d]154Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32EA [auth i]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38061 
Go to UniProtKB:  P38061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38061
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AFA [auth j]107Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05744 
Go to UniProtKB:  P05744
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05744
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AGA [auth l]120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX84 
Go to UniProtKB:  P0CX84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX84
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AHA [auth m]100Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05745 
Go to UniProtKB:  P05745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05745
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AIA [auth n]88Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49166 
Go to UniProtKB:  P49166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49166
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
25S rRNA3,396Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNA158Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
ITS2 RNA232Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary