Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A)

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 

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Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs.

Tang, L.El-Din, T.M.Swanson, T.M.Pryde, D.C.Scheuer, T.Zheng, N.Catterall, W.A.

(2016) Nature 537: 117-121

  • DOI: https://doi.org/10.1038/nature19102
  • Primary Citation of Related Structures:  
    5KLB, 5KLG, 5KLS, 5KMD, 5KMF, 5KMH

  • PubMed Abstract: 

    Ca 2+ antagonist drugs are widely used in therapy of cardiovascular disorders. Three chemical classes of drugs bind to three separate, but allosterically interacting, receptor sites on Ca V 1.2 channels, the most prominent voltage-gated Ca 2+ (Ca V ) channel type in myocytes in cardiac and vascular smooth muscle. The 1,4-dihydropyridines are used primarily for treatment of hypertension and angina pectoris and are thought to act as allosteric modulators of voltage-dependent Ca 2+ channel activation, whereas phenylalkylamines and benzothiazepines are used primarily for treatment of cardiac arrhythmias and are thought to physically block the pore. The structural basis for the different binding, action, and therapeutic uses of these drugs remains unknown. Here we present crystallographic and functional analyses of drug binding to the bacterial homotetrameric model Ca V channel Ca V Ab, which is inhibited by dihydropyridines and phenylalkylamines with nanomolar affinity in a state-dependent manner. The binding site for amlodipine and other dihydropyridines is located on the external, lipid-facing surface of the pore module, positioned at the interface of two subunits. Dihydropyridine binding allosterically induces an asymmetric conformation of the selectivity filter, in which partially dehydrated Ca 2+ interacts directly with one subunit and blocks the pore. In contrast, the phenylalkylamine Br-verapamil binds in the central cavity of the pore on the intracellular side of the selectivity filter, physically blocking the ion-conducting pathway. Structure-based mutations of key amino-acid residues confirm drug binding at both sites. Our results define the structural basis for binding of dihydropyridines and phenylalkylamines at their distinct receptor sites on Ca V channels and offer key insights into their fundamental mechanisms of action and differential therapeutic uses in cardiovascular diseases.

  • Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, Washington 98195-7280, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein
A, B, C, D
285Aliarcobacter butzleri RM4018Mutation(s): 0 
Gene Names: Abu_1752
Membrane Entity: Yes 
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018))
Explore A8EVM5 
Go to UniProtKB:  A8EVM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8EVM5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MC3

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
FA [auth D],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
C36 H72 N O8 P
Query on CPS

Download Ideal Coordinates CCD File 
GA [auth D]
H [auth A]
I [auth A]
J [auth A]
Q [auth B]
GA [auth D],
H [auth A],
I [auth A],
J [auth A],
Q [auth B],
R [auth B]
C32 H58 N2 O7 S
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
Z [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.9α = 90
b = 125.7β = 90
c = 191.485γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL112808
National Research Service AwardUnited StatesT32GM008268

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description