7W7F | pdb_00007w7f

Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431

PDB DOI: https://doi.org/10.2210/pdb7W7F/pdb
EM Map EMD-32343: EMDB EMDataResource

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

Deposited: 2021-12-04 Released: 2022-04-06
Deposition Author(s): Jiang, D., Li, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for modulation of human Na V 1.3 by clinical drug and selective antagonist.

Li, X., Xu, F., Xu, H., Zhang, S., Gao, Y., Zhang, H., Dong, Y., Zheng, Y., Yang, B., Sun, J., Zhang, X.C., Zhao, Y., Jiang, D.

(2022) Nat Commun 13: 1286-1286

PubMed: 35277491 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-28808-5
Primary Citation Related Structures:
7W77, 7W7F

PubMed Abstract:
Voltage-gated sodium (Na _V) channels play fundamental roles in initiating and propagating action potentials. Na _V1.3 is involved in numerous physiological processes including neuronal development, hormone secretion and pain perception. Here we report structures of human Na _V1.3/β1/β2 in complex with clinically-used drug bulleyaconitine A and selective antagonist ICA121431. Bulleyaconitine A is located around domain I-II fenestration, providing the detailed view of the site-2 neurotoxin binding site. It partially blocks ion path and expands the pore-lining helices, elucidating how the bulleyaconitine A reduces peak amplitude but improves channel open probability. In contrast, ICA121431 preferentially binds to activated domain IV voltage-sensor, consequently strengthens the Ile-Phe-Met motif binding to its receptor site, stabilizes the channel in inactivated state, revealing an allosterically inhibitory mechanism of Na _V channels. Our results provide structural details of distinct small-molecular modulators binding sites, elucidate molecular mechanisms of their action on Na _V channels and pave a way for subtype-selective therapeutic development.

Organizational Affiliation

Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.

Macromolecule Content

Total Structure Weight: 290.92 kDa
Atom Count: 11,987
Modeled Residue Count: 1,424
Deposited Residue Count: 2,433
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel subunit beta-1	A [auth B]	218	Homo sapiens	Mutation(s): 0 Gene Names: SCN1B Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q07699 (Homo sapiens) Explore Q07699 Go to UniProtKB: Q07699
PHAROS: Q07699 GTEx: ENSG00000105711
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07699
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth B]	Go to GlyGen: Q07699-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel subunit beta-2	B [auth C]	215	Homo sapiens	Mutation(s): 0 Gene Names: SCN2B Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O60939 (Homo sapiens) Explore O60939 Go to UniProtKB: O60939
PHAROS: O60939 GTEx: ENSG00000149575
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60939
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 3 subunit alpha	C [auth D]	2,000	Homo sapiens	Mutation(s): 0 Gene Names: SCN3A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY46 (Homo sapiens) Explore Q9NY46 Go to UniProtKB: Q9NY46
PHAROS: Q9NY46 GTEx: ENSG00000153253
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NY46
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C [auth D]	Go to GlyGen: Q9NY46-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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 E]	3		N-Glycosylation	Interactions Focus chain D [auth E] Interactions & Density Focus chain D [auth E]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 [auth F]	2		N-Glycosylation	Interactions Focus chain E [auth F] Interactions & Density Focus chain E [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6OU Query on 6OU Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain K [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain K [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain K [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] K [auth D] M [auth D] AA [auth D], BA [auth D], CA [auth D], K [auth D], M [auth D], N [auth D], O [auth D], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate C₃₉ H₇₆ N O₈ P FHQVHHIBKUMWTI-OTMQOFQLSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain K [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [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 AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain K [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
9Z9 Query on 9Z9 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en C₃₄ H₅₆ O₅ CEEBZAXXSRFQIC-GZSGZGDASA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
8DE (Subject of Investigation/LOI) Query on 8DE Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	2,2-diphenyl-~{N}-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]ethanamide C₂₃ H₁₉ N₃ O₃ S₂ URSQNPPONHUJDL-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain J [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], H [auth B], I [auth B], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth D]