2I2R

Crystal structure of the KChIP1/Kv4.3 T1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Three-dimensional structure of the KChIP1-Kv4.3 T1 complex reveals a cross-shaped octamer

Pioletti, M.Findeisen, F.Hura, G.L.Minor Jr., D.L.

(2006) Nat Struct Mol Biol 13: 987-995

  • DOI: https://doi.org/10.1038/nsmb1164
  • Primary Citation of Related Structures:  
    2I2R

  • PubMed Abstract: 

    Brain I(A) and cardiac I(to) currents arise from complexes containing Kv4 voltage-gated potassium channels and cytoplasmic calcium-sensor proteins (KChIPs). Here, we present X-ray crystallographic and small-angle X-ray scattering data that show that the KChIP1-Kv4.3 N-terminal cytoplasmic domain complex is a cross-shaped octamer bearing two principal interaction sites. Site 1 comprises interactions between a unique Kv4 channel N-terminal hydrophobic segment and a hydrophobic pocket formed by displacement of the KChIP H10 helix. Site 2 comprises interactions between a T1 assembly domain loop and the KChIP H2 helix. Functional and biochemical studies indicate that site 1 influences channel trafficking, whereas site 2 affects channel gating, and that calcium binding is intimately linked to KChIP folding and complex formation. Together, the data resolve how Kv4 channels and KChIPs interact and provide a framework for understanding how KChIPs modulate Kv4 function.


  • Organizational Affiliation

    Cardiovascular Research Institute, Department of Biochemistry, California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143-2532, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily D member 3
A, B, C, D, I
A, B, C, D, I, J, K, L
144Rattus norvegicusMutation(s): 0 
Gene Names: Kcnd3
UniProt
Find proteins for Q62897 (Rattus norvegicus)
Explore Q62897 
Go to UniProtKB:  Q62897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62897
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kv channel-interacting protein 1
E, F, G, H, M
E, F, G, H, M, N, O, P
180Homo sapiensMutation(s): 2 
Gene Names: KCNIP1KCHIP1VABP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZI2 (Homo sapiens)
Explore Q9NZI2 
Go to UniProtKB:  Q9NZI2
PHAROS:  Q9NZI2
GTEx:  ENSG00000182132 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZI2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
GA [auth I]
HA [auth J]
IA [auth K]
JA [auth L]
Q [auth A]
GA [auth I],
HA [auth J],
IA [auth K],
JA [auth L],
Q [auth A],
R [auth B],
S [auth C],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
DA [auth H]
EA [auth H]
KA [auth M]
AA [auth G],
BA [auth G],
DA [auth H],
EA [auth H],
KA [auth M],
LA [auth M],
MA [auth N],
NA [auth N],
OA [auth O],
PA [auth O],
QA [auth P],
RA [auth P],
U [auth E],
V [auth E],
X [auth F],
Y [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth G],
FA [auth H],
W [auth E],
Z [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.151α = 91
b = 98.105β = 112.56
c = 97.783γ = 111.77
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description