8E59

Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone at 3.1 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the severe adverse interaction of sofosbuvir and amiodarone on L-type Ca v channels.

Yao, X.Gao, S.Wang, J.Li, Z.Huang, J.Wang, Y.Wang, Z.Chen, J.Fan, X.Wang, W.Jin, X.Pan, X.Yu, Y.Lagrutta, A.Yan, N.

(2022) Cell 185: 4801-4810.e13

  • DOI: https://doi.org/10.1016/j.cell.2022.10.024
  • Primary Citation of Related Structures:  
    8E56, 8E57, 8E58, 8E59, 8E5A, 8E5B

  • PubMed Abstract: 

    Drug-drug interaction of the antiviral sofosbuvir and the antiarrhythmics amiodarone has been reported to cause fatal heartbeat slowing. Sofosbuvir and its analog, MNI-1, were reported to potentiate the inhibition of cardiomyocyte calcium handling by amiodarone, which functions as a multi-channel antagonist, and implicate its inhibitory effect on L-type Ca v channels, but the molecular mechanism has remained unclear. Here we present systematic cryo-EM structural analysis of Ca v 1.1 and Ca v 1.3 treated with amiodarone or sofosbuvir alone, or sofosbuvir/MNI-1 combined with amiodarone. Whereas amiodarone alone occupies the dihydropyridine binding site, sofosbuvir is not found in the channel when applied on its own. In the presence of amiodarone, sofosbuvir/MNI-1 is anchored in the central cavity of the pore domain through specific interaction with amiodarone and directly obstructs the ion permeation path. Our study reveals the molecular basis for the physical, pharmacodynamic interaction of two drugs on the scaffold of Ca v channels.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1D2,161Homo sapiensMutation(s): 0 
Gene Names: CACNA1DCACH3CACN4CACNL1A2CCHL1A2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01668 (Homo sapiens)
Explore Q01668 
Go to UniProtKB:  Q01668
PHAROS:  Q01668
GTEx:  ENSG00000157388 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01668
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1B [auth D]1,103Homo 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: 6Go to GlyGen: P54289-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-3484Homo sapiensMutation(s): 0 
Gene Names: CACNB3CACNLB3
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
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseD [auth B]3N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, H
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D 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
F
4N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G01361SX
GlyCosmos:  G01361SX
GlyGen:  G01361SX
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
K [auth A]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
BBI (Subject of Investigation/LOI)
Query on BBI

Download Ideal Coordinates CCD File 
I [auth A](2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone
C25 H29 I2 N O3
IYIKLHRQXLHMJQ-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth D],
M [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],
N [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BBI BindingDB:  8E59 IC50: min: 270, max: 1900 (nM) from 2 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM130762

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references