7W9K | pdb_00007w9k

Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7W9K

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 300.56 kDa 
  • Atom Count: 14,933 
  • Modeled Residue Count: 1,705 
  • Deposited Residue Count: 2,464 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alpha2,031Homo sapiensMutation(s): 0 
Gene Names: SCN9ANENA
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15858
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q15858-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  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: 4Go to GlyGen: Q07699-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S

Query on P5S



Download:Ideal Coordinates CCD File
H [auth A],
KA [auth A],
Y [auth A]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
PCW

Query on PCW



Download:Ideal Coordinates CCD File
IA [auth A],
JA [auth A],
U [auth A],
X [auth A],
Z [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
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
LPE

Query on LPE



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
MA [auth A],
Q [auth A],
QA [auth B],
R [auth A],
T [auth A],
V [auth A],
W [auth A]
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C26 H57 N O6 P
XKBJVQHMEXMFDZ-AREMUKBSSA-O
Y01

Query on Y01



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
LA [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
LA [auth A],
M [auth A],
O [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
1PW

Query on 1PW



Download:Ideal Coordinates CCD File
S [auth A](2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C20 H40 N O6 P
HWPZKJVGDYNEAW-QUDYQQOWSA-N
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
N [auth A],
NA [auth B],
OA [auth B],
PA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
P [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2022-06-01
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-18
    Changes: Data collection