5KMH

Structure of CavAb in complex with Br-verapamil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/nature19102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ca2+ 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 CaV1.2 channels, the most prominent voltage-gated Ca2+ (CaV) chann ...

    Ca2+ 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 CaV1.2 channels, the most prominent voltage-gated Ca2+ (CaV) 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 Ca2+ 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 CaV channel CaVAb, 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 Ca2+ 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 CaV 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport protein
A, B, C, D
285Arcobacter butzleri (strain RM4018)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Calcium Ion-Selective
Protein: 
Voltage-Gated Calcium Channel (CaV) created by mutation of the NaVAb channel
Find proteins for A8EVM5 (Arcobacter butzleri (strain RM4018))
Go to UniProtKB:  A8EVM5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MC3
Query on MC3

Download SDF File 
Download CCD File 
A, B, D
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
 Ligand Interaction
6U8
Query on 6U8

Download SDF File 
Download CCD File 
C
(2~{R})-2-(2-bromophenyl)-5-[2-(3,4-dimethoxyphenyl)ethyl-methyl-amino]-2-propan-2-yl-pentanenitrile
C25 H33 Br N2 O2
KXOBUGZMWSPKEA-RUZDIDTESA-N
 Ligand Interaction
PX6
Query on PX6

Download SDF File 
Download CCD File 
A, B, C, D
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
C35 H68 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.251 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 125.535α = 90.00
b = 125.525β = 90.00
c = 191.960γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
HKL-2000data reduction
REFMACrefinement
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesR01HL112808
National Research Service AwardUnited StatesT32GM008268

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2016-09-14
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations