9ITI | pdb_00009iti

Nav1.7 with mutations that eliminate beta1 binding

PDB DOI: https://doi.org/10.2210/pdb9ITI/pdb
EM Map EMD-60867: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes MemProtMD

Deposited: 2024-07-20 Released: 2025-08-20
Deposition Author(s): Yan, N., Li, Z., Wu, T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 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

Critical role of extracellular loops in differential modulations of TTX-sensitive and TTX-resistant Na v channels.

Wu, T., Yang, X., Jin, X., Yan, N., Li, Z.

(2025) Proc Natl Acad Sci U S A 122: e2510355122-e2510355122

PubMed: 40768348 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2510355122
Primary Citation Related Structures:
9ITH, 9ITI

PubMed Abstract:
The cardiac voltage-gated sodium channel Na _v1.5 is resistant to tetrodotoxin (TTXr). Here, we report a cryo-electron microscopy (cryo-EM) structure of wild-type human Na _v1.5, coexpressed with the β1 auxiliary subunit and treated with high-concentration TTX, at 3.4 Å resolution. Structural comparison reveals the molecular determinants for the distinct responses to TTX as well as β subunits between TTXr and TTX-sensitive (TTXs) Na _v channels. A conserved cation-π interaction between the guanidinium group of TTX and Tyr or Phe on the P2 _I helix in TTXs Na _v channels is lost in all TTXr subtypes owing to the replacement by Cys/Ser at the corresponding locus, explaining their differential TTX sensitivities. The β1 subunit is invisible in the EM map. Comparison of Na _v1.5 with Na _v1.7 and Na _v1.8, which are, respectively, TTXs and TTXr, identifies four sites on the extracellular loops (ECLs) that may account for their different β1-binding abilities. When the corresponding residues in TTXs Na _v1.7 are replaced with those from Na _v1.5, the modulatory effects of β1 on channel activation and inactivation are diminished. Consistently, β1 is absent in the 3D EM reconstruction of this Na _v1.7 mutant. Together with our previous structure-guided discovery that TTXr channels lack a Cys on the ECL _II for disulfide bond formation with β2 or β4, the structure-function relationship studies underscore the importance of the ECLs in the mechanistic distinctions between TTXs and TTXr Na _v channels. The ECLs may be further explored for the development of subtype-specific drugs.

Organizational Affiliation

State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 245.99 kDa
Atom Count: 11,086
Modeled Residue Count: 1,268
Deposited Residue Count: 2,030
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 9 subunit alpha	A	2,030	Homo sapiens	Mutation(s): 11 Gene Names: SCN9A, NENA Membrane Entity: Yes
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

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
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 P [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth A] mmCIF format, chain F [auth A]	F [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 F [auth A] Focus chain P [auth A] Interactions & Density Focus chain F [auth A] Focus chain P [auth A]
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain L [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A]	L [auth A], O [auth A], Q [auth A], W [auth A], X [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain L [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain L [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain W [auth A] Focus chain X [auth A]
9Z9 Query on 9Z9 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]	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en C₃₄ H₅₆ O₅ CEEBZAXXSRFQIC-GZSGZGDASA-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 V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth A] M [auth A] N [auth A] H [auth A], I [auth A], K [auth A], M [auth A], N [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain CA [auth A] SDF format, chain BA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A]	BA [auth A], CA [auth A], Y [auth A], Z [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
1PW Query on 1PW 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]	(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate C₂₀ H₄₀ N O₆ P HWPZKJVGDYNEAW-QUDYQQOWSA-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 E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]