9AYL

Cryo-EM structure of human Cav3.2 with ACT-709478


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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 for human Ca v 3.2 inhibition by selective antagonists.

Huang, J.Fan, X.Jin, X.Lyu, C.Guo, Q.Liu, T.Chen, J.Davakan, A.Lory, P.Yan, N.

(2024) Cell Res 34: 440-450

  • DOI: https://doi.org/10.1038/s41422-024-00959-8
  • Primary Citation of Related Structures:  
    9AYG, 9AYH, 9AYJ, 9AYK, 9AYL

  • PubMed Abstract: 

    The Ca v 3.2 subtype of T-type calcium channels has been targeted for developing analgesics and anti-epileptics for its role in pain and epilepsy. Here we present the cryo-EM structures of Ca v 3.2 alone and in complex with four T-type calcium channel selective antagonists with overall resolutions ranging from 2.8 Å to 3.2 Å. The four compounds display two binding poses. ACT-709478 and TTA-A2 both place their cyclopropylphenyl-containing ends in the central cavity to directly obstruct ion flow, meanwhile extending their polar tails into the IV-I fenestration. TTA-P2 and ML218 project their 3,5-dichlorobenzamide groups into the II-III fenestration and place their hydrophobic tails in the cavity to impede ion permeation. The fenestration-penetrating mode immediately affords an explanation for the state-dependent activities of these antagonists. Structure-guided mutational analysis identifies several key residues that determine the T-type preference of these drugs. The structures also suggest the role of an endogenous lipid in stabilizing drug binding in the central cavity.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent T-type calcium channel subunit alpha-1H2,116Homo sapiensMutation(s): 0 
Gene Names: CACNA1H
UniProt & NIH Common Fund Data Resources
Find proteins for O95180 (Homo sapiens)
Explore O95180 
Go to UniProtKB:  O95180
PHAROS:  O95180
GTEx:  ENSG00000196557 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95180
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JL3
Query on JL3

Download Ideal Coordinates CCD File 
H [auth A],
J [auth A],
K [auth A],
L [auth A]
[(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate
C35 H70 N O8 P
SKVKIGSFTGVBOX-MGBGTMOVSA-N
LPE
Query on LPE

Download Ideal Coordinates CCD File 
F [auth A]1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C26 H57 N O6 P
XKBJVQHMEXMFDZ-AREMUKBSSA-O
Y01
Query on Y01

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
M [auth A],
N [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
A1AHK (Subject of Investigation/LOI)
Query on A1AHK

Download Ideal Coordinates CCD File 
B [auth A]N-{1-[(5-cyanopyridin-2-yl)methyl]-1H-pyrazol-3-yl}-2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}acetamide
C22 H18 F3 N5 O
LSYANGLAZUZYFX-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Human Frontier Science Program (HFSP)FranceLT000754/2020-L

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary