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 8WE8 | pdb_00008we8

Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine, amlodipine and pinaverium at 2.9 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WE8

This is version 1.2 of the entry. See complete history. 

Literature

Structural basis for human Ca v 1.2 inhibition by multiple drugs and the neurotoxin calciseptine.

Gao, S., Yao, X., Chen, J., Huang, G., Fan, X., Xue, L., Li, Z., Wu, T., Zheng, Y., Huang, J., Jin, X., Wang, Y., Wang, Z., Yu, Y., Liu, L., Pan, X., Song, C., Yan, N.

(2023) Cell 186: 5363-5374.e16

  • DOI: https://doi.org/10.1016/j.cell.2023.10.007
  • Primary Citation Related Structures: 
    8FHS, 8WE6, 8WE7, 8WE8, 8WE9, 8WEA

  • PubMed Abstract: 

    Ca v 1.2 channels play crucial roles in various neuronal and physiological processes. Here, we present cryo-EM structures of human Ca v 1.2, both in its apo form and in complex with several drugs, as well as the peptide neurotoxin calciseptine. Most structures, apo or bound to calciseptine, amlodipine, or a combination of amiodarone and sofosbuvir, exhibit a consistent inactivated conformation with a sealed gate, three up voltage-sensing domains (VSDs), and a down VSD II . Calciseptine sits on the shoulder of the pore domain, away from the permeation path. In contrast, when pinaverium bromide, an antispasmodic drug, is inserted into a cavity reminiscent of the IFM-binding site in Na v channels, a series of structural changes occur, including upward movement of VSD II coupled with dilation of the selectivity filter and its surrounding segments in repeat III. Meanwhile, S4-5 III merges with S5 III to become a single helix, resulting in a widened but still non-conductive intracellular gate.


  • Organizational Affiliation: 
    • Department of Urology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: gaoshuai812@whu.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 440.82 kDa 
  • Atom Count: 21,309 
  • Modeled Residue Count: 2,593 
  • Deposited Residue Count: 3,848 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1C2,201Homo sapiensMutation(s): 0 
Gene Names: CACNA1C, CACH2, CACN2, CACNL1A1, CCHL1A1
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q13936-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1B [auth D]1,103Homo sapiensMutation(s): 0 
Gene Names: CACNA2D1, CACNL2A, CCHL2A, MHS3
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: 7Go to GlyGen: P54289-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-3484Homo sapiensMutation(s): 0 
Gene Names: CACNB3
UniProt & NIH Common Fund Data Resources
Find proteins for P54284 (Homo sapiens)
Explore P54284 
Go to UniProtKB:  P54284
PHAROS:  P54284
GTEx:  ENSG00000167535 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54284
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
CalciseptinD [auth B]60Dendroaspis polylepis polylepisMutation(s): 0 
UniProt
Find proteins for P22947 (Dendroaspis polylepis polylepis)
Explore P22947 
Go to UniProtKB:  P22947
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22947
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G01361SX
GlyCosmos: G01361SX
GlyGen: G01361SX

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT5

Query on PT5



Download:Ideal Coordinates CCD File
P [auth A][(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-HJBQCNPJSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
Q [auth A]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
6UB

Query on 6UB



Download:Ideal Coordinates CCD File
R [auth A]amlodipine
C20 H25 Cl N2 O5
HTIQEAQVCYTUBX-KRWDZBQOSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
O [auth A],
T [auth D],
U [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
S [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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
Beijing Nova ProgramChinaZ191100001119127

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-18
    Changes: Data collection