7YG5

Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the topiramate-bound state

PDB DOI: https://doi.org/10.2210/pdb7YG5/pdb
EM Map EMD-33808: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2022-07-11 Released: 2023-11-29
Deposition Author(s): Gao, Y., Zhao, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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 insights into allosteric effects of antiepileptic drug topiramate on CaV2.3 channel.

Gao, Y., Zhao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 463.73 kDa
Atom Count: 20,308
Modelled Residue Count: 2,436
Deposited Residue Count: 4,014
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent R-type calcium channel subunit alpha-1E	A	2,313	Homo sapiens	Mutation(s): 0 Gene Names: CACNA1E, CACH6, CACNL1A6 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q15878 (Homo sapiens) Explore Q15878 Go to UniProtKB: Q15878
PHAROS: Q15878 GTEx: ENSG00000198216
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15878
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit beta-1	B	598	Homo sapiens	Mutation(s): 0 Gene Names: CACNB1, CACNLB1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q02641 (Homo sapiens) Explore Q02641 Go to UniProtKB: Q02641
PHAROS: Q02641 GTEx: ENSG00000067191
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02641
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel subunit alpha-2/delta-1	C [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54289
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth E], E [auth C]	3		N-Glycosylation	Interactions Focus chain D [auth E] Focus chain E [auth C] Interactions & Density Focus chain D [auth E] Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G44266EX GlyCosmos: G44266EX GlyGen: G44266EX

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	J [auth A], K [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain W [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth A]	G [auth A] L [auth A] N [auth A] P [auth A] Q [auth A] G [auth A], L [auth A], N [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], W [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain G [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth A] Interactions & Density Focus chain G [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth A]
TOR (Subject of Investigation/LOI) Query on TOR Download Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A]	V [auth A]	[(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate C₁₂ H₂₁ N O₈ S KJADKKWYZYXHBB-XBWDGYHZSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	H [auth A] I [auth A] M [auth A] O [auth A] X [auth A] H [auth A], I [auth A], M [auth A], O [auth A], X [auth A], Y [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain X [auth A] Focus chain Y [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain Z [auth D] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth D]	U [auth A], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain Z [auth D] Interactions & Density Focus chain U [auth A] Focus chain Z [auth D]