5X0M | pdb_00005x0m

Structure of a eukaryotic voltage-gated sodium channel at near atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb5X0M/pdb
• EM Map EMD-6698: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Periplaneta americana
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-01-21 Released: 2017-03-08 
• Deposition Author(s): Shen, H., Zhou, Q., Pan, X., Li, Z., Wu, J., Yan, N.
• Funding Organization(s): the Ministry of Science and Technology of China, the National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.

Shen, H., Zhou, Q., Pan, X., Li, Z., Wu, J., Yan, N.

(2017) Science 355

• PubMed: 28183995 
• DOI: https://doi.org/10.1126/science.aal4326
• Primary Citation Related Structures: 
  5X0M


• PubMed Abstract: 
  

  Voltage-gated sodium (Na _v ) channels are responsible for the initiation and propagation of action potentials. They are associated with a variety of channelopathies and are targeted by multiple pharmaceutical drugs and natural toxins. Here, we report the cryogenic electron microscopy structure of a putative Na _v channel from American cockroach (designated Na _v PaS) at 3.8 angstrom resolution. The voltage-sensing domains (VSDs) of the four repeats exhibit distinct conformations. The entrance to the asymmetric selectivity filter vestibule is guarded by heavily glycosylated and disulfide bond-stabilized extracellular loops. On the cytoplasmic side, a conserved amino-terminal domain is placed below VSD _I , and a carboxy-terminal domain binds to the III-IV linker. The structure of Na _v PaS establishes an important foundation for understanding function and disease mechanism of Na _v and related voltage-gated calcium channels.

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Organizational Affiliation: 
• State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.
Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 187.78 kDa 
• Atom Count: 10,654 
• Modeled Residue Count: 1,323 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein	A	1,596	Periplaneta americana	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0E0C2 (Periplaneta americana) Explore D0E0C2  Go to UniProtKB:  D0E0C2
Glycosylation
Glycosylation Sites: 7

Oligosaccharides

Help  

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Shen, H., Zhou, Q., Pan, X., Li, Z., Wu, J., Yan, N.

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Funding Organization	Location	Grant Number
the Ministry of Science and Technology of China	China	2015CB910101, 2016YFA0500402, 2014ZX09507003-006
the National Natural Science Foundation of China	China	projects 31621092, 31630017, and 31611130036

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Other
• Version 1.2: 2019-12-11
  Changes: Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary