5XGS | pdb_00005xgs

Crystal structure of human WBSCR16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.218 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human WBSCR16, an RCC1-like protein in mitochondria

Koyama, M.Sasaki, T.Sasaki, N.Matsuura, Y.

(2017) Protein Sci 26: 1870-1877

  • DOI: https://doi.org/10.1002/pro.3210
  • Primary Citation Related Structures: 
    5XGS

  • PubMed Abstract: 

    WBSCR16 (Williams-Beuren Syndrome Chromosomal Region 16) gene is located in a large deletion region of Williams-Beuren syndrome (WBS), which is a neurodevelopmental disorder. Although the relationship between WBSCR16 and WBS remains unclear, it has been reported that WBSCR16 is a member of a functional module that regulates mitochondrial 16S rRNA abundance and intra-mitochondrial translation. WBSCR16 has RCC1 (Regulator of Chromosome Condensation 1)-like amino acid sequence repeats but the function of WBSCR16 appears to be different from that of other RCC1 superfamily members. Here, we demonstrate that WBSCR16 localizes to mitochondria in HeLa cells, and report the crystal structure of WBSCR16 determined to 2.0 Å resolution using multi-wavelength anomalous diffraction. WBSCR16 adopts the seven-bladed β-propeller fold characteristic of RCC1-like proteins. A comparison of the WBSCR16 structure with that of RCC1 and other RCC1-like proteins reveals that, although many of the residues buried in the core of the β-propeller are highly conserved, the surface residues are poorly conserved and conformationally divergent.


  • Organizational Affiliation
    • Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Japan.

Macromolecule Content 

  • Total Structure Weight: 91.84 kDa 
  • Atom Count: 6,614 
  • Modeled Residue Count: 796 
  • Deposited Residue Count: 854 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RCC1-like G exchanging factor-like protein
A, B
427Homo sapiensMutation(s): 0 
Gene Names: RCC1LWBSCR16
UniProt & NIH Common Fund Data Resources
Find proteins for Q96I51 (Homo sapiens)
Explore Q96I51 
Go to UniProtKB:  Q96I51
PHAROS:  Q96I51
GTEx:  ENSG00000274523 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96I51
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.02α = 90
b = 54.55β = 95.82
c = 140.473γ = 90
Software Package:
Software NamePurpose
MOSFLMdata collection
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CRANKphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references