5Z1G

Structure of the Brx1 and Ebp2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein EBP2
A, C
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EBP2YKL172WYKL636
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BRX1
B, D
234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRX1YOL077C
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.934α = 90
b = 47.353β = 94.1
c = 100.695γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

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: 2024-03-27
    Changes: Data collection, Database references