8HMA | pdb_00008hma

Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with tetrandrine (TET)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8HMA

This is version 1.2 of the entry. See complete history

Literature

Structural bases of inhibitory mechanism of Ca V 1.2 channel inhibitors.

Wei, Y.Yu, Z.Wang, L.Li, X.Li, N.Bai, Q.Wang, Y.Li, R.Meng, Y.Xu, H.Wang, X.Dong, Y.Huang, Z.Zhang, X.C.Zhao, Y.

(2024) Nat Commun 15: 2772-2772

  • DOI: https://doi.org/10.1038/s41467-024-47116-8
  • Primary Citation Related Structures: 
    8HLP, 8HMA, 8HMB

  • PubMed Abstract: 

    The voltage-gated calcium channel Ca V 1.2 is essential for cardiac and vessel smooth muscle contractility and brain function. Accumulating evidence demonstrates that malfunctions of Ca V 1.2 are involved in brain and heart diseases. Pharmacological inhibition of Ca V 1.2 is therefore of therapeutic value. Here, we report cryo-EM structures of Ca V 1.2 in the absence or presence of the antirheumatic drug tetrandrine or antihypertensive drug benidipine. Tetrandrine acts as a pore blocker in a pocket composed of S6 II , S6 III , and S6 IV helices and forms extensive hydrophobic interactions with Ca V 1.2. Our structure elucidates that benidipine is located in the D III -D IV fenestration site. Its hydrophobic sidechain, phenylpiperidine, is positioned at the exterior of the pore domain and cradled within a hydrophobic pocket formed by S5 DIII , S6 DIII , and S6 DIV helices, providing additional interactions to exert inhibitory effects on both L-type and T-type voltage gated calcium channels. These findings provide the structural foundation for the rational design and optimization of therapeutic inhibitors of voltage-gated calcium channels.


  • Organizational Affiliation
    • Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content 

  • Total Structure Weight: 441.88 kDa 
  • Atom Count: 19,101 
  • Modeled Residue Count: 2,333 
  • Deposited Residue Count: 3,876 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alphaA [auth E]2,173Homo sapiensMutation(s): 0 
Gene Names: CACNA1C
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13936 (Homo sapiens)
Explore Q13936 
Go to UniProtKB:  Q13936
PHAROS:  Q13936
GTEx:  ENSG00000151067 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13936
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2c of Voltage-dependent L-type calcium channel subunit beta-2B [auth H]632Homo sapiensMutation(s): 0 
Gene Names: CACNB2CACNLB2MYSB
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08289 (Homo sapiens)
Explore Q08289 
Go to UniProtKB:  Q08289
PHAROS:  Q08289
GTEx:  ENSG00000165995 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08289
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1C [auth F]1,071Homo sapiensMutation(s): 0 
Gene Names: CACNA2D1CACNL2ACCHL2AMHS3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P54289 (Homo sapiens)
Explore P54289 
Go to UniProtKB:  P54289
PHAROS:  P54289
GTEx:  ENSG00000153956 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54289
Glycosylation
Glycosylation Sites: 9Go to GlyGen: P54289-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
E,
F [auth E],
H [auth E]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
A1AC9
(Subject of Investigation/LOI)

Query on A1AC9



Download:Ideal Coordinates CCD File
G [auth E]6,6',7,12-tetramethoxy-2,2'-dimethyl-1beta-3,4-didehydroberbaman
C38 H40 N2 O6
OUHWUXGBWHCKDH-UFXYQILXSA-N
R16

Query on R16



Download:Ideal Coordinates CCD File
D [auth E]HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
K [auth F]
L [auth F]
M [auth F]
N [auth F]
P [auth F]
K [auth F],
L [auth F],
M [auth F],
N [auth F],
P [auth F],
Q [auth F],
R [auth F],
S [auth F],
T [auth F],
U [auth F],
V [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA

Query on BMA



Download:Ideal Coordinates CCD File
O [auth F]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth E],
J [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-04
    Changes: Data collection