5XQH | pdb_00005xqh

Crystal structure of truncated human Rogdi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.247 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.204 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5XQH

This is version 1.1 of the entry. See complete history

Literature

The crystal structure of human Rogdi provides insight into the causes of Kohlschutter-Tonz Syndrome

Lee, H.Jeong, H.Choe, J.Jun, Y.Lim, C.Lee, C.

(2017) Sci Rep 7: 3972-3972

  • DOI: https://doi.org/10.1038/s41598-017-04120-x
  • Primary Citation Related Structures: 
    5XQH, 5XQI

  • PubMed Abstract: 

    Kohlschutter-Tönz syndrome (KTS) is a rare autosomal-recessive disorder of childhood onset characterized by global developmental delay, spasticity, epilepsy, and amelogenesis imperfecta. Rogdi, an essential protein, is highly conserved across metazoans, and mutations in Rogdi are linked to KTS. However, how certain mutations in Rogdi abolish its physiological functions and cause KTS is not known. In this study, we determined the crystal structure of human Rogdi protein at atomic resolution. Rogdi forms a novel elongated curved structure comprising the α domain, a leucine-zipper-like four-helix bundle, and a characteristic β-sheet domain. Within the α domain, the N-terminal H1 helix (residues 19-45) pairs with the C-terminal H6 helix (residues 252-287) in an antiparallel manner, indicating that the integrity of the four-helix bundle requires both N- and C-terminal residues. The crystal structure, in conjunction with biochemical data, indicates that the α domain might undergo a conformational change and provide a structural platform for protein-protein interactions. Disruption of the four-helix bundle by mutation results in significant destabilization of the structure. This study provides structural insights into how certain mutations in Rogdi affect its structure and cause KTS, which has important implications for the development of pharmaceutical agents against this debilitating neurological disease.


  • Organizational Affiliation
    • Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan, 44919, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 30.33 kDa 
  • Atom Count: 1,929 
  • Modeled Residue Count: 223 
  • Deposited Residue Count: 268 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein rogdi homolog268Homo sapiensMutation(s): 0 
Gene Names: ROGDI
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZN7 (Homo sapiens)
Explore Q9GZN7 
Go to UniProtKB:  Q9GZN7
PHAROS:  Q9GZN7
GTEx:  ENSG00000067836 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZN7
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.247 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.204 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.364α = 90
b = 114.695β = 90
c = 44.205γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
Cootmodel building
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary