9LHZ | pdb_00009lhz

Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and sea anemone toxin Av3

PDB DOI: https://doi.org/10.2210/pdb9LHZ/pdb
EM Map EMD-63108: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Periplaneta americana, Anemonia sulcata
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2025-01-13 Released: 2026-02-04
Deposition Author(s): Jiang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9LHZ

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

Literature

Structure of voltage-gated sodium channel NavPas and sea anemone toxin Av3

Jiang, H.

To be published.

Macromolecule Content

Total Structure Weight: 189.33 kDa
Atom Count: 10,753
Modeled Residue Count: 1,349
Deposited Residue Count: 1,623
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein PaFPC1	A	1,596	Periplaneta americana	Mutation(s): 0
UniProt
Find proteins for D0E0C2 (Periplaneta americana) Explore D0E0C2 Go to UniProtKB: D0E0C2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0E0C2
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta-actitoxin-Avd2a	B [auth H]	27	Anemonia sulcata	Mutation(s): 0
UniProt
Find proteins for P01535 (Anemonia sulcata) Explore P01535 Go to UniProtKB: P01535
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01535
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	5		N-Glycosylation	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G89225LT GlyCosmos: G89225LT GlyGen: G89225LT

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 [auth F]	2		N-Glycosylation	Interactions Focus chain D [auth F] Interactions & Density Focus chain D [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LPE Query on LPE Download:Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF format, chain H	H	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain H Interactions & Density Focus chain H
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32372580

Revision History (Full details and data files)

Version 1.0: 2026-02-04
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.