6NT3 | pdb_00006nt3

Cryo-EM structure of a human-cockroach hybrid Nav channel.

PDB DOI: https://doi.org/10.2210/pdb6NT3/pdb
EM Map EMD-0500: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Periplaneta americana, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2019-01-28 Released: 2019-02-20
Deposition Author(s): Clairfeuille, T., Rohou, A., Payandeh, J.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 4.2 of the entry. See complete history.

Literature

Cryo-EM structures of a human-cockroach hybrid Nav channel in the presence and absence of the alpha-scorpion toxin AaH2.

Clairfeuille, T., Rohou, A., Payandeh, J.

(2019) Science

Macromolecule Content

Total Structure Weight: 186.82 kDa
Atom Count: 10,934
Modeled Residue Count: 1,278
Deposited Residue Count: 1,559
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, Sodium channel protein PaFPC1, chimeric construct	A	1,559	Periplaneta americana, Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for D0E0C2 (Periplaneta americana) Explore D0E0C2 Go to UniProtKB: D0E0C2
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 Groups	D0E0C2 Q15858
Glycosylation
Glycosylation Sites: 6	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
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G61217QH GlyCosmos: G61217QH GlyGen: G61217QH

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJP Query on AJP Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	Digitonin C₅₆ H₉₂ O₂₉ UVYVLBIGDKGWPX-KUAJCENISA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
76F Query on 76F Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	(7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate C₄₁ H₇₆ N O₈ P SUGLKZVXTGKYMP-QNGDKYGQSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
LHG Query on LHG 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]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [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] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cisTEM

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

Clairfeuille, T.

Rohou, A.

Payandeh, J.

Revision History (Full details and data files)

Version 1.0: 2019-02-20
Type: Initial release
Version 1.1: 2019-12-18
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2021-08-18
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 4.0: 2021-08-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 4.1: 2024-10-23
Changes: Data collection, Structure summary
Version 4.2: 2025-05-28
Changes: Data collection