21TQ | pdb_000021tq

The structure of Nav1.7 with veratridine standing near the IFM motif (site I)

PDB DOI: https://doi.org/10.2210/pdb21TQ/pdb
EM Map EMD-67991: EMDB EMDataResource

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

Deposited: 2025-12-24 Released: 2026-03-11
Deposition Author(s): Fan, X., Huang, J., Yan, N.
Funding Organization(s): Human Frontier Science Program (HFSP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 Å
Resolution: 2.70 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

Open-state structure of veratridine-activated human Nav1.7 reveals the molecular choreography of fast inactivation

Fan, X., Chen, J., Xue, L., Wang, H., Wu, T., Huang, X., Lu, F., Jin, X., Song, C., Huang, J., Yan, N.

To be published.

Macromolecule Content

Total Structure Weight: 271.91 kDa
Atom Count: 13,098
Modeled Residue Count: 1,538
Deposited Residue Count: 2,280
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 regulatory subunit beta-1	A [auth B]	173	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 A [auth B]	Go to GlyGen: Q07699-1
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 regulatory subunit beta-2	B [auth C]	119	Homo sapiens	Mutation(s): 0 Gene Names: SCN2B, UNQ326/PRO386
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60939
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 9 subunit alpha	C [auth A]	1,988	Homo sapiens	Mutation(s): 0 Gene Names: SCN9A, NENA
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens) Explore Q15858 Go to UniProtKB: Q15858
PHAROS: Q15858 GTEx: ENSG00000169432
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15858
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C [auth A]	Go to GlyGen: Q15858-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	D, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain V [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A]	S [auth A], V [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain S [auth A] Focus chain V [auth A] Interactions & Density Focus chain S [auth A] Focus chain V [auth A]
A1E26 (Subject of Investigation/LOI) Query on A1E26 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]	Veratridine C₃₆ H₅₁ N O₁₁ FVECELJHCSPHKY-YFUMOZOISA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
P3X Query on P3X Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [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 AA [auth A] Interactions & Density Focus chain AA [auth A]
LPE Query on LPE Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain I [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain I [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	I [auth B] Q [auth A] R [auth A] T [auth A] U [auth A] I [auth B], Q [auth A], R [auth A], T [auth A], U [auth A], W [auth A], X [auth A], Y [auth A]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain I [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain I [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Z [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth A]	N [auth A], O [auth A], P [auth A], Z [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain G [auth B]	F [auth B] G [auth B] H [auth B] J [auth A] K [auth A] F [auth B], G [auth B], H [auth B], J [auth A], K [auth A], L [auth A]	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 J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]