25IH | pdb_000025ih

Cryo-EM structure of human Nav1.6 in complex with Cn2

PDB DOI: https://doi.org/10.2210/pdb25IH/pdb
EM Map EMD-80133: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Centruroides noxius
Expression System: Homo sapiens, Centruroides noxius
Mutation(s): Yes

Deposited: 2026-04-06 Released: 2026-05-20
Deposition Author(s): Fan, X., Huang, J., Yan, N.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 25IH

This is version 1.0 of the entry. See complete history.

Literature

Diverse modulation mechanisms of human Nav1.6 by gating modifier neurotoxins

Fan, X., Jian, H., Yang, L., Chen, J., Wang, H., Huang, X., Geng, J., Wu, Q., Xie, Y., Lu, F., Guo, Q., Shen, Z., Jin, X., Yan, N.

To be published.

Macromolecule Content

Total Structure Weight: 272.07 kDa
Atom Count: 12,745
Modeled Residue Count: 1,468
Deposited Residue Count: 2,265
Unique protein chains: 3

Macromolecules

Find similar proteins by:

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
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:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel regulatory subunit beta-1	B [auth C]	218	Homo sapiens	Mutation(s): 0 Gene Names: SCN1B
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

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-mammal toxin Cn2	C [auth D]	67	Centruroides noxius	Mutation(s): 1
UniProt
Find proteins for P01495 (Centruroides noxius) Explore P01495 Go to UniProtKB: P01495
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01495
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
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-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	9		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

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]

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)]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-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth G]	9		N-Glycosylation	Interactions Focus chain F [auth G] Interactions & Density Focus chain F [auth G]

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT5 Query on PT5 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	[(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 Z [auth D] Interactions & Density Focus chain Z [auth D]
P5S Query on P5S Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [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 P [auth A] Interactions & Density Focus chain P [auth A]
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain U [auth A] SDF format, chain Y [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth A] MOL2 format, chain Y [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain U [auth A] mmCIF format, chain Y [auth D]	K [auth A], N [auth A], O [auth A], U [auth A], Y [auth D]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain K [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth A] Focus chain Y [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth A] Focus chain Y [auth D]
P3X Query on P3X Download:Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [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 S [auth A] Interactions & Density Focus chain S [auth A]
9Z9 Query on 9Z9 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]	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en C₃₄ H₅₆ O₅ CEEBZAXXSRFQIC-GZSGZGDASA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
LPE Query on LPE Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A]	L [auth A], R [auth A], T [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain L [auth A] Focus chain R [auth A] Focus chain T [auth A] Interactions & Density Focus chain L [auth A] Focus chain R [auth A] Focus chain T [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	G [auth A] H [auth A] I [auth A] V [auth C] W [auth C] G [auth A], H [auth A], I [auth A], V [auth C], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32330052, 32322039, 32271252, and 32501082

Revision History (Full details and data files)

Version 1.0: 2026-05-20
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.