6NT3

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  OPMPDBTMMemProtMDmpstruc


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

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Experimental Data Snapshot

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

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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 186.82 kDa 
• Atom Count: 10,934 
• Modelled Residue Count: 1,278 
• Deposited Residue Count: 1,559 
• Unique protein chains: 1

Macromolecules

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 Q15858 (Homo sapiens) Explore Q15858  Go to UniProtKB:  Q15858
PHAROS:  Q15858 GTEx:  ENSG00000169432
Find proteins for D0E0C2 (Periplaneta americana) Explore D0E0C2  Go to UniProtKB:  D0E0C2
UniProt Groups	D0E0C2Q15858

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
Glycosylation Resources
GlyTouCan:  G61217QH GlyCosmos:  G61217QH GlyGen:  G61217QH

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AJP	O [auth A]	Digitonin C56 H92 O29 UVYVLBIGDKGWPX-KUAJCENISA-N
76F	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
LHG	N [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
Y01	I [auth A]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
NAG	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

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
RECONSTRUCTION	cisTEM

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Clairfeuille, T., Rohou, A., Payandeh, J.

Revision History  

• 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