7UHF | pdb_00007uhf

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

PDB DOI: https://doi.org/10.2210/pdb7UHF/pdb
EM Map EMD-26513: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

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 1.3 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 32: 946-948

PubMed: 35477996 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00663-5
Primary Citation Related Structures:
7UHF, 7UHG

Organizational Affiliation

Department of Molecular Biology, Princeton University, Princeton, NJ, USA. xiayao@princeton.edu.

Macromolecule Content

Total Structure Weight: 429.8 kDa
Atom Count: 20,379
Modeled Residue Count: 2,502
Deposited Residue Count: 3,748
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit alpha-1D	A	2,161	Homo sapiens	Mutation(s): 0 Gene Names: CACNA1D, CACH3, CACN4, CACNL1A2, CCHL1A2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01668
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel subunit alpha-2/delta-1	B [auth D]	1,103	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54289
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain B [auth D]	Go to GlyGen: P54289-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit beta-3	C	484	Homo sapiens	Mutation(s): 0 Gene Names: CACNB3, CACNLB3
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54284
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D [auth B]	3		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	4		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
N90 (Subject of Investigation/LOI) Query on N90 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1-(diphenylmethyl)-4-[(2E)-3-phenylprop-2-en-1-yl]piperazine C₂₆ H₂₈ N₂ DERZBLKQOCDDDZ-JLHYYAGUSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain J [auth A] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	J [auth A], N [auth D], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain J [auth A] Focus chain N [auth D] Focus chain O [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth D] MOL2 format, chain K [auth A] MOL2 format, chain P [auth D] mmCIF format, chain K [auth A] mmCIF format, chain P [auth D]	K [auth A], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth D] Interactions & Density Focus chain K [auth A] Focus chain P [auth D]