8X93

P/Q type calcium channel in complex with omega-Agatoxin IVA

PDB DOI: https://doi.org/10.2210/pdb8X93/pdb
EM Map EMD-38160: EMDB EMDataResource

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

Deposited: 2023-11-29 Released: 2024-03-20
Deposition Author(s): Yan, N., Li, Z., Cong, Y., Wu, T., Wang, T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 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 different omega-agatoxin IVA sensitivities of the P-type and Q-type Ca v 2.1 channels.

Li, Z., Cong, Y., Wu, T., Wang, T., Lou, X., Yang, X., Yan, N.

(2024) Cell Res

PubMed: 38443561 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-024-00940-5
Primary Citation of Related Structures:
8X90, 8X91, 8X93

Organizational Affiliation

Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. lizhangq@tsinghua.edu.cn.

Macromolecule Content

Total Structure Weight: 478.56 kDa
Atom Count: 21,976
Modelled Residue Count: 2,659
Deposited Residue Count: 4,160
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 L-type calcium channel subunit beta-3	A [auth C]	496	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54284
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 calcium channel subunit alpha-2/delta-1	B	1,115	Homo sapiens	Mutation(s): 0 Gene Names: CACNA2D1, CACNL2A, CCHL2A, MHS3
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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent P/Q-type calcium channel subunit alpha-1A	C [auth A]	2,549	Homo sapiens	Mutation(s): 0 Gene Names: CACNA1A, CACH4, CACN3, CACNL1A4
UniProt & NIH Common Fund Data Resources
Find proteins for O00555 (Homo sapiens) Explore O00555 Go to UniProtKB: O00555
PHAROS: O00555 GTEx: ENSG00000141837
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00555
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth E]	3		N-Glycosylation	Interactions Focus chain D [auth E] Interactions & Density Focus chain D [auth E]
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth F], G [auth H], H [auth I]	2		N-Glycosylation	Interactions Focus chain E [auth F] Focus chain G [auth H] Focus chain H [auth I] Interactions & Density Focus chain E [auth F] Focus chain G [auth H] Focus chain H [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 [auth G]	4		N-Glycosylation	Interactions Focus chain F [auth G] Interactions & Density Focus chain F [auth G]
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT5 Query on PT5 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate C₄₇ H₈₅ O₁₉ P₃ CNWINRVXAYPOMW-HJBQCNPJSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A]	V [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	O [auth A], R [auth A], S [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain O [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain O [auth A] Focus chain R [auth A] Focus chain S [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	K [auth A], P [auth A], Q [auth A], T [auth A], U [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain K [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain K [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth A] Focus chain U [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth A]	J [auth B], N [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth B] Focus chain N [auth A] Interactions & Density Focus chain J [auth B] Focus chain N [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth A] SDF format, chain W [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth A] MOL2 format, chain W [auth A]	I [auth B], M [auth A], W [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain M [auth A] Focus chain W [auth A] Interactions & Density Focus chain I [auth B] Focus chain M [auth A] Focus chain W [auth A]