6J8G

Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (Y1755 up)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of human Nav1.7 channel in complex with auxiliary subunits and animal toxins.

Shen, H.Liu, D.Wu, K.Lei, J.Yan, N.

(2019) Science 363: 1303-1308

  • DOI: 10.1126/science.aaw2493
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Voltage-gated sodium channel Na <sub>v </sub>1.7 represents a promising target for pain relief. Here we report the cryo-electron microscopy structures of the human Na <sub>v </sub>1.7-β1-β2 complex bound to two combinations of pore blockers and gatin ...

    Voltage-gated sodium channel Na v 1.7 represents a promising target for pain relief. Here we report the cryo-electron microscopy structures of the human Na v 1.7-β1-β2 complex bound to two combinations of pore blockers and gating modifier toxins (GMTs), tetrodotoxin with protoxin-II and saxitoxin with huwentoxin-IV, both determined at overall resolutions of 3.2 angstroms. The two structures are nearly identical except for minor shifts of voltage-sensing domain II (VSD II ), whose S3-S4 linker accommodates the two GMTs in a similar manner. One additional protoxin-II sits on top of the S3-S4 linker in VSD IV The structures may represent an inactivated state with all four VSDs "up" and the intracellular gate closed. The structures illuminate the path toward mechanistic understanding of the function and disease of Na v 1.7 and establish the foundation for structure-aided development of analgesics.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China. nyan@princeton.edu.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Medical Research Center, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium channel subunit beta-2
C
215Homo sapiensMutation(s): 0 
Gene Names: SCN2B
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.7 with β1β2 subunits in complex with huwentoxin-IV and saxitoxin (Y1755 up)
Find proteins for O60939 (Homo sapiens)
Go to Gene View: SCN2B
Go to UniProtKB:  O60939
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium channel protein type 9 subunit alpha
A
2031Homo sapiensMutation(s): 0 
Gene Names: SCN9A (NENA)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.7 with β1β2 subunits in complex with huwentoxin-IV and saxitoxin (Y1755 up)
Find proteins for Q15858 (Homo sapiens)
Go to Gene View: SCN9A
Go to UniProtKB:  Q15858
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sodium channel subunit beta-1
B
218Homo sapiensMutation(s): 0 
Gene Names: SCN1B
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.7 with β1β2 subunits in complex with huwentoxin-IV and saxitoxin (Y1755 up)
Find proteins for Q07699 (Homo sapiens)
Go to Gene View: SCN1B
Go to UniProtKB:  Q07699
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9SL
Query on 9SL

Download SDF File 
Download CCD File 
A
[(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate
Saxitoxin
C10 H17 N7 O4
RPQXVSUAYFXFJA-HGRQIUPRSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2015CB910101
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 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references