7XLQ | pdb_00007xlq

Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the ligand-free (apo) state

PDB DOI: https://doi.org/10.2210/pdb7XLQ/pdb
EM Map EMD-33285: EMDB EMDataResource

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

Deposited: 2022-04-22 Released: 2023-02-08
Deposition Author(s): Gao, Y., Qiu, Y., Wei, Y., Dong, Y., Zhang, X.C., Zhao, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular insights into the gating mechanisms of voltage-gated calcium channel Ca V 2.3.

Gao, Y., Xu, S., Cui, X., Xu, H., Qiu, Y., Wei, Y., Dong, Y., Zhu, B., Peng, C., Liu, S., Zhang, X.C., Sun, J., Huang, Z., Zhao, Y.

(2023) Nat Commun 14: 516-516

PubMed: 36720859 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-36260-2
Primary Citation Related Structures:
7XLQ

PubMed Abstract:
High-voltage-activated R-type Ca _V2.3 channel plays pivotal roles in many physiological activities and is implicated in epilepsy, convulsions, and other neurodevelopmental impairments. Here, we determine the high-resolution cryo-electron microscopy (cryo-EM) structure of human Ca _V2.3 in complex with the α2δ1 and β1 subunits. The VSD _II is stabilized in the resting state. Electrophysiological experiments elucidate that the VSD _II is not required for channel activation, whereas the other VSDs are essential for channel opening. The intracellular gate is blocked by the W-helix. A pre-W-helix adjacent to the W-helix can significantly regulate closed-state inactivation (CSI) by modulating the association and dissociation of the W-helix with the gate. Electrostatic interactions formed between the negatively charged domain on S6 _II, which is exclusively conserved in the Ca _V2 family, and nearby regions at the alpha-interacting domain (AID) and S4-S5 _II helix are identified. Further functional analyses indicate that these interactions are critical for the open-state inactivation (OSI) of Ca _V2 channels.

Organizational Affiliation

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 458.75 kDa
Atom Count: 20,132
Modeled Residue Count: 2,436
Deposited Residue Count: 3,988
Unique protein chains: 3

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15878
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]	1,077	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: 11	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-1	C [auth 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02641
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain U [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain U [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain U [auth A]	G [auth A] J [auth A] L [auth A] N [auth A] P [auth A] G [auth A], J [auth A], L [auth A], N [auth A], P [auth A], U [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain U [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain U [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 K [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A]	H [auth A] I [auth A] K [auth A] M [auth A] Q [auth A] H [auth A], I [auth A], K [auth A], M [auth A], Q [auth A], R [auth A], T [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	BA [auth D] CA [auth D] DA [auth D] V [auth D] W [auth D] BA [auth D], CA [auth D], DA [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain S [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain S [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain S [auth A]	AA [auth D], S [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain S [auth A] Interactions & Density Focus chain AA [auth D] Focus chain S [auth A]