3IF8 | pdb_00003if8

Crystal Structure of ZWILCH, a member of the RZZ kinetochore complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.274 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3IF8

This is version 1.2 of the entry. See complete history

Literature

Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery.

Civril, F.Wehenkel, A.Giorgi, F.M.Santaguida, S.Di Fonzo, A.Grigorean, G.Ciccarelli, F.D.Musacchio, A.

(2010) Structure 18: 616-626

  • DOI: https://doi.org/10.1016/j.str.2010.02.014
  • Primary Citation Related Structures: 
    3IF8

  • PubMed Abstract: 

    The RZZ complex recruits dynein to kinetochores. We investigated structure, topology, and interactions of the RZZ subunits (ROD, ZWILCH, and ZW10) in vitro, in vivo, and in silico. We identify neuroblastoma-amplified gene (NAG), a ZW10 binder, as a ROD homolog. ROD and NAG contain an N-terminal beta propeller followed by an alpha solenoid, which is the architecture of certain nucleoporins and vesicle coat subunits, suggesting a distant evolutionary relationship. ZW10 binding to ROD and NAG is mutually exclusive. The resulting ZW10 complexes (RZZ and NRZ) respectively contain ZWILCH and RINT1 as additional subunits. The X-ray structure of ZWILCH, the first for an RZZ subunit, reveals a novel fold distinct from RINT1's. The evolutionarily conserved NRZ likely acts as a tethering complex for retrograde trafficking of COPI vesicles from the Golgi to the endoplasmic reticulum. The RZZ, limited to metazoans, probably evolved from the NRZ, exploiting the dynein-binding capacity of ZW10 to direct dynein to kinetochores.


  • Organizational Affiliation
    • Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, I-20139 Milan, Italy.

Macromolecule Content 

  • Total Structure Weight: 67.72 kDa 
  • Atom Count: 4,006 
  • Modeled Residue Count: 502 
  • Deposited Residue Count: 596 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein zwilch homolog339Homo sapiensMutation(s): 0 
Gene Names: ZWILCH
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H900 (Homo sapiens)
Explore Q9H900 
Go to UniProtKB:  Q9H900
PHAROS:  Q9H900
GTEx:  ENSG00000174442 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H900
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein zwilch homolog257Homo sapiensMutation(s): 0 
Gene Names: ZWILCH
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H900 (Homo sapiens)
Explore Q9H900 
Go to UniProtKB:  Q9H900
PHAROS:  Q9H900
GTEx:  ENSG00000174442 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H900
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.6α = 90
b = 86.6β = 90
c = 166.89γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations