7WE4

sodium channel I

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structural basis for high-voltage activation and subtype-specific inhibition of human Na v 1.8.

Huang, X., Jin, X., Huang, G., Huang, J., Wu, T., Li, Z., Chen, J., Kong, F., Pan, X., Yan, N.

(2022) Proc Natl Acad Sci U S A 119: e2208211119-e2208211119

  • DOI: 10.1073/pnas.2208211119
  • Primary Citation of Related Structures:  
    7WE4, 7WEL, 7WFR, 7WFW

  • PubMed Abstract: 

    • The dorsal root ganglia-localized voltage-gated sodium (Na v ) channel Na v 1.8 represents a promising target for developing next-generation analgesics. A prominent characteristic of Na v 1.8 is the requirement of more depolarized membrane potential for activation ...

    The dorsal root ganglia-localized voltage-gated sodium (Na v ) channel Na v 1.8 represents a promising target for developing next-generation analgesics. A prominent characteristic of Na v 1.8 is the requirement of more depolarized membrane potential for activation. Here we present the cryogenic electron microscopy structures of human Na v 1.8 alone and bound to a selective pore blocker, A-803467, at overall resolutions of 2.7 to 3.2 Å. The first voltage-sensing domain (VSD I ) displays three different conformations. Structure-guided mutagenesis identified the extracellular interface between VSD I and the pore domain (PD) to be a determinant for the high-voltage dependence of activation. A-803467 was clearly resolved in the central cavity of the PD, clenching S6 IV . Our structure-guided functional characterizations show that two nonligand binding residues, Thr397 on S6 I and Gly1406 on S6 III , allosterically modulate the channel's sensitivity to A-803467. Comparison of available structures of human Na v channels suggests the extracellular loop region to be a potential site for developing subtype-specific pore-blocking biologics.

    Organizational Affiliation: 

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel protein type 10 subunit alphaA1956Homo sapiensMutation(s): 0 
Gene Names: SCN10A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y9 (Homo sapiens)
Explore Q9Y5Y9 
Go to UniProtKB:  Q9Y5Y9
PHAROS:  Q9Y5Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5Y9
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB, C 2N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P5S
Query on P5S
Download Ideal Coordinates CCD File 
AA [auth A],
Y [auth A],
Z [auth A]		O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N		 Ligand Interaction
PCW
Query on PCW
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
M [auth A],
P [auth A],
Q [auth A]		1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O		 Ligand Interaction
LPE
Query on LPE
Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
N [auth A],
O [auth A],
R [auth A],
K [auth A],
L [auth A],
N [auth A],
O [auth A],
R [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C26 H57 N O6 P
XKBJVQHMEXMFDZ-AREMUKBSSA-O		 Ligand Interaction
CLR
Query on CLR
Download Ideal Coordinates CCD File 
BA [auth A],
H [auth A],
S [auth A],
X [auth A]		CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N		 Ligand Interaction
95T (Subject of Investigation/LOI)
Query on 95T
Download Ideal Coordinates CCD File 
G [auth A]5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide
C19 H16 Cl N O4
VHKBTPQDHDSBSP-UHFFFAOYSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release