21TP | pdb_000021tp

Open-state structure of veratridine-activated human Nav1.7

PDB DOI: https://doi.org/10.2210/pdb21TP/pdb
EM Map EMD-67990: EMDB EMDataResource

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

Deposited: 2025-12-24 Released: 2026-03-25
Deposition Author(s): Fan, X., Huang, J., Yan, N.
Funding Organization(s): Human Frontier Science Program (HFSP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Resolution: 3.00 Å
Resolution: 3.00 Å
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 21TP

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: 271.25 kDa
Atom Count: 12,524
Modeled Residue Count: 1,472
Deposited Residue Count: 2,280
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 9 subunit alpha	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15858
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: Q15858-1
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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07699
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain B	Go to GlyGen: Q07699-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel regulatory subunit beta-2	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60939
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain N [auth A]	N [auth A], Q [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain N [auth A] Focus chain Q [auth A] Interactions & Density Focus chain N [auth A] Focus chain Q [auth A]
A1E26 Query on A1E26 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]	Veratridine C₃₆ H₅₁ N O₁₁ FVECELJHCSPHKY-YFUMOZOISA-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 Z [auth B] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A] M [auth A] O [auth A] P [auth A] R [auth A] L [auth A], M [auth A], O [auth A], P [auth A], R [auth A], S [auth A], T [auth A], Z [auth B]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth B]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain U [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain U [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A], U [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] W [auth B] X [auth B] F [auth A], G [auth A], H [auth A], W [auth B], X [auth B], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Resolution: 3.00 Å
Resolution: 3.00 Å
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Human Frontier Science Program (HFSP)	France	LT000754/2020-L

Revision History (Full details and data files)

Version 1.0: 2026-03-25
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.