6U39

2.4 Angstrom crystal structure of the D129G Ca-CaM:CaV1.2 IQ domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca2+binding and cause misfolding.

Wang, K.Brohus, M.Holt, C.Overgaard, M.T.Wimmer, R.Van Petegem, F.

(2020) J Physiol 598: 1169-1186

  • DOI: 10.1113/JP279307
  • Primary Citation of Related Structures:  
    6U39, 6U3A, 6U3B, 6U3D

  • PubMed Abstract: 
  • Mutations in the calmodulin protein (CaM) are associated with arrhythmia syndromes. This study focuses on understanding the structural characteristics of CaM disease mutants and their interactions with the voltage-gated calcium channel Ca V 1 ...

    Mutations in the calmodulin protein (CaM) are associated with arrhythmia syndromes. This study focuses on understanding the structural characteristics of CaM disease mutants and their interactions with the voltage-gated calcium channel Ca V 1.2. Arrhythmia mutations in CaM can lead to loss of Ca 2+ binding, uncoupling of Ca 2+ binding cooperativity, misfolding of the EF-hands and altered affinity for the calcium channel. These results help us to understand how different CaM mutants have distinct effects on structure and interactions with protein targets to cause disease.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, V6T 1Z3 Vancouver, BC, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-1
A, C, E, G, I, K, M, O, Q, S
A, C, E, G, I, K, M, O, Q, S
148Homo sapiensMutation(s): 1 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1C
B, D, F, H, J, L, N, P, R, T
B, D, F, H, J, L, N, P, R, T
37Homo sapiensMutation(s): 0 
Gene Names: CACNA1CCACH2CACN2CACNL1A1CCHL1A1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13936 (Homo sapiens)
Explore Q13936 
Go to UniProtKB:  Q13936
PHAROS:  Q13936
GTEx:  ENSG00000151067 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13936
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth G],
EA [auth G],
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth G],
EA [auth G],
FA [auth G],
GA [auth I],
HA [auth I],
IA [auth K],
JA [auth K],
KA [auth K],
LA [auth M],
MA [auth M],
NA [auth M],
OA [auth O],
PA [auth O],
QA [auth O],
RA [auth Q],
SA [auth Q],
TA [auth Q],
U [auth A],
UA [auth S],
V [auth A],
VA [auth S],
W [auth A],
WA [auth S],
X [auth C],
Y [auth C],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.795α = 90
b = 161.656β = 90
c = 96.277γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references