7XVF

Nav1.7 mutant class2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na v 1.7.

Huang, G.Wu, Q.Li, Z.Jin, X.Huang, X.Wu, T.Pan, X.Yan, N.

(2022) Proc Natl Acad Sci U S A 119: e2209164119-e2209164119

  • DOI: https://doi.org/10.1073/pnas.2209164119
  • Primary Citation of Related Structures:  
    7XVE, 7XVF

  • PubMed Abstract: 

    Voltage-gated sodium (Na v ) channel Na v 1.7 has been targeted for the development of nonaddictive pain killers. Structures of Na v 1.7 in distinct functional states will offer an advanced mechanistic understanding and aid drug discovery. Here we report the cryoelectron microscopy analysis of a human Na v 1.7 variant that, with 11 rationally introduced point mutations, has a markedly right-shifted activation voltage curve with V 1/2 reaching 69 mV. The voltage-sensing domain in the first repeat (VSD I ) in a 2.7-Å resolution structure displays a completely down (deactivated) conformation. Compared to the structure of WT Na v 1.7, three gating charge (GC) residues in VSD I are transferred to the cytosolic side through a combination of helix unwinding and spiral sliding of S4 I and ∼20° domain rotation. A conserved WNФФD motif on the cytoplasmic end of S3 I  stabilizes the down conformation of VSD I . One GC residue is transferred in VSD II mainly through helix sliding. Accompanying GC transfer in VSD I and VSD II , rearrangement and contraction of the intracellular gate is achieved through concerted movements of adjacent segments, including S4-5 I , S4-5 II , S5 II , and all S6 segments. Our studies provide important insight into the electromechanical coupling mechanism of the single-chain voltage-gated ion channels and afford molecular interpretations for a number of pain-associated mutations whose pathogenic mechanism cannot be revealed from previously reported Na v structures.


  • Organizational Affiliation

    Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alpha2,022Homo sapiensMutation(s): 11 
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
Sequence Annotations
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  • Reference Sequence
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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
Sequence Annotations
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  • Reference Sequence
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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

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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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S
Query on P5S

Download Ideal Coordinates CCD File 
JA [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 
HA [auth A]
IA [auth A]
N [auth A]
Q [auth A]
R [auth A]
HA [auth A],
IA [auth A],
N [auth A],
Q [auth A],
R [auth A],
S [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
LPE
Query on LPE

Download Ideal Coordinates CCD File 
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
J [auth A]
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
J [auth A],
K [auth A],
KA [auth A],
M [auth A],
O [auth A],
P [auth A],
PA [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [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 
AA [auth A],
BA [auth A],
CA [auth A],
H [auth A],
Z [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
1PW
Query on 1PW

Download Ideal Coordinates CCD File 
L [auth A](2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C20 H40 N O6 P
HWPZKJVGDYNEAW-QUDYQQOWSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
I [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
LA [auth B]
MA [auth B]
NA [auth B]
F [auth A],
G [auth A],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
QA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Princeton UniversityUnited StatesShirley M. Tilghman endowed professorship
Beijing Municipal Science and Technology CommissionChinaZ191100001119127

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references