8FD7

Structure of the human L-type voltage-gated calcium channel Cav1.2 complexed with gabapentin

PDB DOI: https://doi.org/10.2210/pdb8FD7/pdb
EM Map EMD-29004: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2022-12-02 Released: 2023-03-22
Deposition Author(s): Chen, Z., Mondal, A., Minor, D.L.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)

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 Ca V alpha 2 delta :gabapentin binding.

Chen, Z., Mondal, A., Minor Jr., D.L.

(2023) Nat Struct Mol Biol 30: 735-739

PubMed: 36973510 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-023-00951-7
Primary Citation of Related Structures:
8FD7

PubMed Abstract:
Gabapentinoid drugs for pain and anxiety act on the Ca _Vα ₂δ-1 and Ca _Vα ₂δ-2 subunits of high-voltage-activated calcium channels (Ca _V1s and Ca _V2s). Here we present the cryo-EM structure of the gabapentin-bound brain and cardiac Ca _V1.2/Ca _Vβ ₃/Ca _Vα ₂δ-1 channel. The data reveal a binding pocket in the Ca _Vα ₂δ-1 dCache1 domain that completely encapsulates gabapentin and define Ca _Vα ₂δ isoform sequence variations that explain the gabapentin binding selectivity of Ca _Vα ₂δ-1 and Ca _Vα ₂δ-2.

Organizational Affiliation

Cardiovascular Research Institute, University of California, San Francisco, CA, USA.

Macromolecule Content

Total Structure Weight: 370.95 kDa
Atom Count: 19,701
Modelled Residue Count: 2,416
Deposited Residue Count: 3,230
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel subunit alpha-2/delta-1	A [auth D]	1,105	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: CACNA2D1, CACNL2A, CCHL2A Membrane Entity: Yes
UniProt
Find proteins for P13806 (Oryctolagus cuniculus) Explore P13806 Go to UniProtKB: P13806
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13806
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth D]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit alpha-1C	B [auth K]	1,648	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit beta-3	C	477	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: CACNB3, CACNLB3
UniProt
Find proteins for P54286 (Oryctolagus cuniculus) Explore P54286 Go to UniProtKB: P54286
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54286
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth F]	2		N/A	Interactions Focus chain D [auth F] Interactions & Density Focus chain D [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WO9 Query on WO9 Download Ideal Coordinates CCD File SDF format, chain P [auth K] MOL2 format, chain P [auth K] mmCIF format, chain P [auth K]	P [auth K]	(2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl heptadecanoate C₃₄ H₆₈ N O₈ P YIIGGWPZRIXGNH-JGCGQSQUSA-N		Interactions Focus chain P [auth K] Interactions & Density Focus chain P [auth K]
YSW Query on YSW Download Ideal Coordinates CCD File SDF format, chain Q [auth K] MOL2 format, chain Q [auth K] mmCIF format, chain Q [auth K]	Q [auth K]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl dodecanoate C₂₉ H₅₈ N O₈ P ZLGYVWRJIZPQMM-MHZLTWQESA-N		Interactions Focus chain Q [auth K] Interactions & Density Focus chain Q [auth K]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain R [auth K] SDF format, chain S [auth K] SDF format, chain T [auth K] MOL2 format, chain R [auth K] MOL2 format, chain S [auth K] MOL2 format, chain T [auth K] mmCIF format, chain R [auth K] mmCIF format, chain S [auth K] mmCIF format, chain T [auth K]	R [auth K], S [auth K], T [auth K]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain R [auth K] Focus chain S [auth K] Focus chain T [auth K] Interactions & Density Focus chain R [auth K] Focus chain S [auth K] Focus chain T [auth K]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain G [auth D] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain E [auth D] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain E [auth D] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	E [auth D] G [auth D] H [auth D] I [auth D] J [auth D] E [auth D], G [auth D], H [auth D], I [auth D], J [auth D], K [auth D], L [auth D], M [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D]
GBN Query on GBN Download Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID C₉ H₁₇ N O₂ UGJMXCAKCUNAIE-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain U [auth K] SDF format, chain V [auth K] MOL2 format, chain N [auth D] MOL2 format, chain U [auth K] MOL2 format, chain V [auth K] mmCIF format, chain N [auth D] mmCIF format, chain U [auth K] mmCIF format, chain V [auth K]	N [auth D], U [auth K], V [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain U [auth K] Focus chain V [auth K] Interactions & Density Focus chain N [auth D] Focus chain U [auth K] Focus chain V [auth K]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
GBN	BindingDB: 8FD7	Ki: 120 (nM) from 1 assay(s)
GBN	BindingDB: 8FD7	IC50: min: 27, max: 8900 (nM) from 4 assay(s)

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

Released Date: 2023-03-22

Deposition Author(s):

Chen, Z.

Mondal, A.

Minor, D.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL080050
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	DC007664