7UHF

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

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-03-26 Released: 2022-05-11 
  • Deposition Author(s): Gao, S., Yao, X., Yan, N.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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 1.0 of the entry. See complete history


Literature

Structural basis for pore blockade of human voltage-gated calcium channel Ca v 1.3 by motion sickness drug cinnarizine.

Yao, X.Gao, S.Yan, N.

(2022) Cell Res 


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1DA2161Homo sapiensMutation(s): 0 
Gene Names: CACNA1DCACH3CACN4CACNL1A2CCHL1A2
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1B [auth D]1103Homo sapiensMutation(s): 0 
Gene Names: CACNA2D1CACNL2ACCHL2AMHS3
UniProt & NIH Common Fund Data Resources
Find proteins for P54289 (Homo sapiens)
Explore P54289 
Go to UniProtKB:  P54289
PHAROS:  P54289
GTEx:  ENSG00000153956 
Entity Groups  
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UniProt GroupP54289
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-3C484Homo 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, G, H 2N/AN-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseF 4N/AN-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
M [auth A]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
Y01
Query on Y01

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L [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
N90 (Subject of Investigation/LOI)
Query on N90

Download Ideal Coordinates CCD File 
I [auth A]1-(diphenylmethyl)-4-[(2E)-3-phenylprop-2-en-1-yl]piperazine
C26 H28 N2
DERZBLKQOCDDDZ-JLHYYAGUSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
K [auth A],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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

  • Deposited Date: 2022-03-26 
  • Released Date: 2022-05-11 
  • Deposition Author(s): Gao, S., Yao, X., Yan, N.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM130762

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release