7W9M

Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (S6IV pi helix conformer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

High-resolution structures of human Na v 1.7 reveal gating modulation through alpha-pi helical transition of S6 IV.

Huang, G.Liu, D.Wang, W.Wu, Q.Chen, J.Pan, X.Shen, H.Yan, N.

(2022) Cell Rep 39: 110735-110735

  • DOI: https://doi.org/10.1016/j.celrep.2022.110735
  • Primary Citation of Related Structures:  
    7W9K, 7W9L, 7W9M, 7W9P, 7W9T

  • PubMed Abstract: 

    Na v 1.7 represents a preeminent target for next-generation analgesics for its critical role in pain sensation. Here we report a 2.2-Å resolution cryo-EM structure of wild-type (WT) Na v 1.7 complexed with the β1 and β2 subunits that reveals several previously indiscernible cytosolic segments. Reprocessing of the cryo-EM data for our reported structures of Na v 1.7(E406K) bound to various toxins identifies two distinct conformations of S6 IV , one composed of α helical turns only and the other containing a π helical turn in the middle. The structure of ligand-free Na v 1.7(E406K), determined at 3.5-Å resolution, is identical to the WT channel, confirming that binding of Huwentoxin IV or Protoxin II to VSD II allosterically induces the α → π transition of S6 IV . The local secondary structural shift leads to contraction of the intracellular gate, closure of the fenestration on the interface of repeats I and IV, and rearrangement of the binding site for the fast inactivation motif.


  • Organizational Affiliation

    Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alpha2,031Homo sapiensMutation(s): 1 
Gene Names: SCN9ANENA
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens)
Go to UniProtKB:  Q15858
PHAROS:  Q15858
GTEx:  ENSG00000169432 
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q15858-1
Sequence Annotations
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  • 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
UniProt & NIH Common Fund Data Resources
Find proteins for Q07699 (Homo sapiens)
Go to UniProtKB:  Q07699
PHAROS:  Q07699
GTEx:  ENSG00000105711 
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q07699-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-2215Homo sapiensMutation(s): 0 
Gene Names: SCN2BUNQ326/PRO386
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O60939 (Homo sapiens)
Explore O60939 
Go to UniProtKB:  O60939
PHAROS:  O60939
GTEx:  ENSG00000149575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60939
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth E],
E [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S
Query on P5S

Download Ideal Coordinates CCD File 
I [auth A]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
LPE
Query on LPE

Download Ideal Coordinates CCD File 
S [auth B]1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C26 H57 N O6 P
XKBJVQHMEXMFDZ-AREMUKBSSA-O
Y01
Query on Y01

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
9SR (Subject of Investigation/LOI)
Query on 9SR

Download Ideal Coordinates CCD File 
F [auth A](1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)
C11 H17 N3 O8
CFMYXEVWODSLAX-QOZOJKKESA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
N [auth A]
P [auth B]
Q [auth B]
G [auth A],
H [auth A],
N [auth A],
P [auth B],
Q [auth B],
R [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9SR BindingDB:  7W9M Kd: 1.8 (nM) from 1 assay(s)
IC50: min: 6, max: 30 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary