4ZGP | pdb_00004zgp

Structure of Cdc123 from Schizosaccharomyces pombe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZGP

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features.

Panvert, M.Dubiez, E.Arnold, L.Perez, J.Mechulam, Y.Seufert, W.Schmitt, E.

(2015) Structure 23: 1596-1608

  • DOI: https://doi.org/10.1016/j.str.2015.06.014
  • Primary Citation Related Structures: 
    4ZGN, 4ZGO, 4ZGP, 4ZGQ

  • PubMed Abstract: 

    Eukaryotic initiation factor 2 (eIF2), a heterotrimeric guanosine triphosphatase, has a central role in protein biosynthesis by supplying methionylated initiator tRNA to the ribosomal translation initiation complex and by serving as a target for translational control in response to stress. Recent work identified a novel step indispensable for eIF2 function: assembly of eIF2 from its three subunits by the cell proliferation protein Cdc123. We report the first crystal structure of a Cdc123 representative, that from Schizosaccharomyces pombe, both isolated and bound to domain III of Saccharomyces cerevisiae eIF2γ. The structures show that Cdc123 resembles enzymes of the ATP-grasp family. Indeed, Cdc123 binds ATP-Mg(2+), and conserved residues contacting ATP-Mg(2+) are essential for Cdc123 to support eIF2 assembly and cell viability. A docking of eIF2αγ onto Cdc123, combined with genetic and biochemical experiments, allows us to propose a model explaining how Cdc123 participates in the biogenesis of eIF2 through facilitating assembly of eIF2γ to eIF2α.


  • Organizational Affiliation
    • Laboratoire de Biochimie, Ecole Polytechnique, CNRS, UMR7654, 91128 Palaiseau Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 68.36 kDa 
  • Atom Count: 4,501 
  • Modeled Residue Count: 496 
  • Deposited Residue Count: 586 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division cycle protein 123
A, B
293Schizosaccharomyces pombeMutation(s): 0 
Gene Names: cdc123SPAP27G11.03
UniProt
Find proteins for Q9P7N5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P7N5 
Go to UniProtKB:  Q9P7N5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P7N5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.483α = 90
b = 91.436β = 91.24
c = 86.006γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CNRSFranceUMR7654
Ecole polytechniqueFranceUMR7654

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description