Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.61 kDa 
• Atom Count: 1294 
• Residue Count: 166 
• Unique protein chains: 2

3DVK

Crystal Structure of Ca2+/CaM-CaV2.3 IQ domain complex

• DOI: 10.2210/pdb3DVK/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-18 Released: 2008-11-04 
• Deposition Author(s): Kim, E.Y., Rumpf, C.H., Fujiwara, Y., Cooley, E.S., Van Petegem, F., Minor, D.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.291 
• R-Value Work: 0.256 
• R-Value Observed: 0.258 

Literature

Structures of Ca(V)2 Ca(2+)/CaM-IQ Domain Complexes Reveal Binding Modes that Underlie Calcium-Dependent Inactivation and Facilitation.

Kim, E.Y., Rumpf, C.H., Fujiwara, Y., Cooley, E.S., Van Petegem, F., Minor, D.L.

(2008) Structure 16: 1455-1467

• PubMed: 18940602 
• DOI: 10.1016/j.str.2008.07.010
• Primary Citation of Related Structures:  
  3DVM, 3DVE, 3DVJ, 3DVK


• PubMed Abstract: 
  

Calcium influx drives two opposing voltage-activated calcium channel (Ca(V)) self-modulatory processes: calcium-dependent inactivation (CDI) and calcium-dependent facilitation (CDF). Specific Ca(2+)/calmodulin (Ca(2+)/CaM) lobes produce CDI and CDF through interactions with the Ca(V)alpha(1) subunit IQ domain. Curiously, Ca(2+)/CaM lobe modulation polarity appears inverted between Ca(V)1s and Ca(V)2s. Here, we present crystal structures of Ca(V)2.1, Ca(V)2.2, and Ca(V)2.3 Ca(2+)/CaM-IQ domain complexes. All display binding orientations opposite to Ca(V)1.2 with a physical reversal of the CaM lobe positions relative to the IQ alpha-helix. Titration calorimetry reveals lobe competition for a high-affinity site common to Ca(V)1 and Ca(V)2 IQ domains that is occupied by the CDI lobe in the structures. Electrophysiological experiments demonstrate that the N-terminal Ca(V)2 Ca(2+)/C-lobe anchors affect CDF. Together, the data unveil the remarkable structural plasticity at the heart of Ca(V) feedback modulation and indicate that Ca(V)1 and Ca(V)2 IQ domains bear a dedicated CDF site that exchanges Ca(2+)/CaM lobe occupants.

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Organizational Affiliation: 

Cardiovascular Research Institute, Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2330, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	A	148	Homo sapiens	Mutation(s): 0  Gene Names:  CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23  Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS:  P0DP23 GTEx:  ENSG00000198668

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent R-type calcium channel subunit alpha-1E	B	23	Rattus norvegicus	Mutation(s): 0  Gene Names: Cacna1e, Cach6, Cacnl1a6
Find proteins for Q07652 (Rattus norvegicus) Explore Q07652  Go to UniProtKB:  Q07652

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.291 
• R-Value Work: 0.256 
• R-Value Observed: 0.258 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.262	α = 90
b = 44.262	β = 90
c = 337.941	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-18 
• Released Date: 2008-11-04 
Deposition Author(s): Kim, E.Y., Rumpf, C.H., Fujiwara, Y., Cooley, E.S., Van Petegem, F., Minor, D.L.

Revision History 

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description