6NT3

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

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 4.1 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 


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alpha, Sodium channel protein PaFPC1, chimeric construct1,559Periplaneta americana, Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsD0E0C2Q15858
Glycosylation
Glycosylation Sites: 6
Go to GlyGen: Q15858-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61217QH
GlyCosmos:  G61217QH
GlyGen:  G61217QH
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP
Download Ideal Coordinates CCD File 
O [auth A]Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
76F
Query on 76F
Download Ideal Coordinates CCD File 
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
Query on LHG
Download Ideal Coordinates CCD File 
N [auth A]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Y01
Query on Y01
Download Ideal Coordinates CCD File 
I [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
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:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

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