9DK5 | pdb_00009dk5

Cryo-EM structure of human Nav1.6 in complex with PaurTx3

PDB DOI: https://doi.org/10.2210/pdb9DK5/pdb
EM Map EMD-46943: EMDB EMDataResource

Classification: TRANSPORT PROTEIN/TOXIN
Organism(s): Homo sapiens, Paraphysa scrofa
Expression System: Homo sapiens, Paraphysa scrofa
Mutation(s): No

Deposited: 2024-09-08 Released: 2025-09-17
Deposition Author(s): Fan, X., Huang, J., Yan, N.
Funding Organization(s): Human Frontier Science Program (HFSP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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

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

Fan, X., Jian, H., Chen, J., Wang, H., Wu, Q., Liu, T., Guo, Q., Shen, Z., Pan, X., Jin, X., Yan, N.

To be published.

Macromolecule Content

Total Structure Weight: 273.51 kDa
Atom Count: 12,873
Modeled Residue Count: 1,517
Deposited Residue Count: 2,300
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 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
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UQD0
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: Q9UQD0-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07699
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain B [auth C]	Go to GlyGen: Q07699-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-theraphotoxin-Ps1a	C [auth H], D [auth I], E [auth J]	34	Paraphysa scrofa	Mutation(s): 0
UniProt
Find proteins for P84510 (Paraphysa scrofa) Explore P84510 Go to UniProtKB: P84510
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84510
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	F [auth D]	9		N-Glycosylation	Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

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