8FHD | pdb_00008fhd

Cryo-EM structure of human voltage-gated sodium channel Nav1.6

PDB DOI: https://doi.org/10.2210/pdb8FHD/pdb
EM Map EMD-29082: EMDB EMDataResource

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

Deposited: 2022-12-14 Released: 2023-02-08
Deposition Author(s): Fan, X., Huang, J., Yan, N.
Funding Organization(s): Human Frontier Science Program (HFSP)

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 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of human voltage-gated sodium channel Na v 1.6.

Fan, X., Huang, J., Jin, X., Yan, N.

(2023) Proc Natl Acad Sci U S A 120: e2220578120-e2220578120

PubMed: 36696443 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2220578120
Primary Citation Related Structures:
8FHD

PubMed Abstract:
Voltage-gated sodium channel Na _v1.6 plays a crucial role in neuronal firing in the central nervous system (CNS). Aberrant function of Na _v1.6 may lead to epilepsy and other neurological disorders. Specific inhibitors of Na _v1.6 thus have therapeutic potentials. Here we present the cryo-EM structure of human Na _v1.6 in the presence of auxiliary subunits β1 and fibroblast growth factor homologous factor 2B (FHF2B) at an overall resolution of 3.1 Å. The overall structure represents an inactivated state with closed pore domain (PD) and all "up" voltage-sensing domains. A conserved carbohydrate-aromatic interaction involving Trp302 and Asn326, together with the β1 subunit, stabilizes the extracellular loop in repeat I. Apart from regular lipids that are resolved in the EM map, an unprecedented Y-shaped density that belongs to an unidentified molecule binds to the PD, revealing a potential site for developing Na _v1.6-specific blockers. Structural mapping of disease-related Na _v1.6 mutations provides insights into their pathogenic mechanism.

Organizational Affiliation

Department of Molecular Biology, Princeton University, Princeton, NJ 08544.

Macromolecule Content

Total Structure Weight: 263.82 kDa
Atom Count: 12,686
Modeled Residue Count: 1,467
Deposited Residue Count: 2,198
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 8 subunit alpha	A	1,980	Homo sapiens	Mutation(s): 0 Gene Names: SCN8A, MED Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQD0 (Homo sapiens) Explore Q9UQD0 Go to UniProtKB: Q9UQD0
PHAROS: Q9UQD0 GTEx: ENSG00000196876
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UQD0
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: Q9UQD0-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel subunit beta-1	B [auth C]	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 B [auth C]	Go to GlyGen: Q07699-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D]	9		N-Glycosylation	Interactions Focus chain C [auth D] Interactions & Density Focus chain C [auth D]
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

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

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P5S Query on P5S Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain W [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth A]	Q [auth A], W [auth A]	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain Q [auth A] Focus chain W [auth A] Interactions & Density Focus chain Q [auth A] Focus chain W [auth A]
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A]	M [auth A], P [auth A], R [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain M [auth A] Focus chain P [auth A] Focus chain R [auth A] Interactions & Density Focus chain M [auth A] Focus chain P [auth A] Focus chain R [auth A]
P3X Query on P3X Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	(5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate C₃₅ H₆₈ N O₈ P IXIBEFBSXYIWMP-VCRBCDDQSA-N		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]
9Z9 Query on 9Z9 Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en C₃₄ H₅₆ O₅ CEEBZAXXSRFQIC-GZSGZGDASA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
LPE Query on LPE Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	L [auth A], N [auth A], O [auth A], S [auth A], T [auth A]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Focus chain T [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	I [auth A], K [auth A], U [auth A], V [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain U [auth A] Focus chain V [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] E [auth A] F [auth A] G [auth A] AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Z [auth C]