7JPW

Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of the Modulation of the Voltage-Gated Calcium Ion Channel Ca v 1.1 by Dihydropyridine Compounds*.

Gao, S.Yan, N.

(2021) Angew Chem Int Ed Engl 60: 3131-3137

  • DOI: 10.1002/anie.202011793
  • Primary Citation of Related Structures:  
    7JPW, 7JPX, 7JPV, 7JPK, 7JPL

  • PubMed Abstract: 
  • 1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca 2+ (Ca v ) channels. DHP compounds exhibit chirality-specific antagonistic or agonistic effects. The structure of rabbit Ca v 1 ...

    1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca 2+ (Ca v ) channels. DHP compounds exhibit chirality-specific antagonistic or agonistic effects. The structure of rabbit Ca v 1.1 bound to an achiral drug nifedipine reveals the general binding mode for DHP drugs, but the molecular basis for chiral specificity remained elusive. Herein, we report five cryo-EM structures of nanodisc-embedded Ca v 1.1 in the presence of the bestselling drug amlodipine, a DHP antagonist (R)-(+)-Bay K8644, and a titration of its agonistic enantiomer (S)-(-)-Bay K8644 at resolutions of 2.9-3.4 Å. The amlodipine-bound structure reveals the molecular basis for the high efficacy of the drug. All structures with the addition of the Bay K8644 enantiomers exhibit similar inactivated conformations, suggesting that (S)-(-)-Bay K8644, when acting as an agonist, is insufficient to lock the activated state of the channel for a prolonged duration.


    Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1SA1873Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNA1SCACH1CACNL1A3
Membrane Entity: Yes 
UniProt
Find proteins for P07293 (Oryctolagus cuniculus)
Explore P07293 
Go to UniProtKB:  P07293
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-1 subunitB [auth E]222Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNG1CACNLG
Membrane Entity: Yes 
UniProt
Find proteins for P19518 (Oryctolagus cuniculus)
Explore P19518 
Go to UniProtKB:  P19518
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1C [auth F]1105Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNA2D1CACNL2ACCHL2A
Membrane Entity: Yes 
UniProt
Find proteins for P13806 (Oryctolagus cuniculus)
Explore P13806 
Go to UniProtKB:  P13806
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1 (Subject of Investigation/LOI)
Query on PC1

Download Ideal Coordinates CCD File 
L [auth A]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
3PE (Subject of Investigation/LOI)
Query on 3PE

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , M [auth A] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  M [auth A],  N [auth A]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
VFY (Subject of Investigation/LOI)
Query on VFY

Download Ideal Coordinates CCD File 
O [auth A]methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate
C16 H16 F3 N2 O4
XGEFGRAURZVVHS-CYBMUJFWSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-08-10 
  • Released Date: 2020-11-18 
  • Deposition Author(s): Yan, N., Gao, S.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDMR-1420541

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Database references