3DRY

X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pentameric assembly of potassium channel tetramerization domain-containing protein 5.

Dementieva, I.S.Tereshko, V.McCrossan, Z.A.Solomaha, E.Araki, D.Xu, C.Grigorieff, N.Goldstein, S.A.

(2009) J Mol Biol 387: 175-191

  • DOI: https://doi.org/10.1016/j.jmb.2009.01.030
  • Primary Citation of Related Structures:  
    3DRX, 3DRY, 3DRZ

  • PubMed Abstract: 

    We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K(+) (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels by approximately 30 degrees; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with approximately 1 microM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.


  • Organizational Affiliation

    Department of Pediatrics and Institute of Molecular Pediatric Sciences, University of Chicago, Chicago, IL 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BTB/POZ domain-containing protein KCTD5
A, B, C, D, E
202Homo sapiensMutation(s): 0 
Gene Names: KCTD5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXV2 (Homo sapiens)
Explore Q9NXV2 
Go to UniProtKB:  Q9NXV2
PHAROS:  Q9NXV2
GTEx:  ENSG00000167977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXV2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.99α = 90
b = 106.791β = 90
c = 110.174γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description