6AGF

Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta 1.

Pan, X.Li, Z.Zhou, Q.Shen, H.Wu, K.Huang, X.Chen, J.Zhang, J.Zhu, X.Lei, J.Xiong, W.Gong, H.Xiao, B.Yan, N.

(2018) Science 362

  • DOI: https://doi.org/10.1126/science.aau2486
  • Primary Citation of Related Structures:  
    6AGF

  • PubMed Abstract: 

    Voltage-gated sodium (Na v ) channels, which are responsible for action potential generation, are implicated in many human diseases. Despite decades of rigorous characterization, the lack of a structure of any human Na v channel has hampered mechanistic understanding. Here, we report the cryo-electron microscopy structure of the human Na v 1.4-β1 complex at 3.2-Å resolution. Accurate model building was made for the pore domain, the voltage-sensing domains, and the β1 subunit, providing insight into the molecular basis for Na + permeation and kinetic asymmetry of the four repeats. Structural analysis of reported functional residues and disease mutations corroborates an allosteric blocking mechanism for fast inactivation of Na v channels. The structure provides a path toward mechanistic investigation of Na v channels and drug discovery for Na v channelopathies.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 4 subunit alpha1,879Homo sapiensMutation(s): 0 
Gene Names: SCN4A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P35499 (Homo sapiens)
Explore P35499 
Go to UniProtKB:  P35499
PHAROS:  P35499
GTEx:  ENSG00000007314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35499
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P35499-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-1218Homo sapiensMutation(s): 0 
Gene Names: SCN1B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07699 (Homo sapiens)
Explore Q07699 
Go to UniProtKB:  Q07699
PHAROS:  Q07699
GTEx:  ENSG00000105711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07699
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q07699-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6OU
Query on 6OU

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
9Z9
Query on 9Z9

Download Ideal Coordinates CCD File 
L [auth A](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2015CB910101
Ministry of Science and Technology (China)China2016YFA0501100
Ministry of Science and Technology (China)China2016YFA0500402
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31630017
National Natural Science Foundation of ChinaChina81861138009

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary