7XMF

Cryo-EM structure of human NaV1.7/beta1/beta2-Nav1.7-IN2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for Na V 1.7 inhibition by pore blockers.

Zhang, J.Shi, Y.Huang, Z.Li, Y.Yang, B.Gong, J.Jiang, D.

(2022) Nat Struct Mol Biol 29: 1208-1216

  • DOI: 10.1038/s41594-022-00860-1
  • Primary Citation of Related Structures:  
    7XM9, 7XMF, 7XMG

  • PubMed Abstract: 
  • Voltage-gated sodium channel Na V 1.7 plays essential roles in pain and odor perception. Na V 1.7 variants cause pain disorders. Accordingly, Na V 1.7 has elicited extensive attention in developing new analgesics. Here we present cryo-EM structures of human Na V 1 ...

    Voltage-gated sodium channel Na V 1.7 plays essential roles in pain and odor perception. Na V 1.7 variants cause pain disorders. Accordingly, Na V 1.7 has elicited extensive attention in developing new analgesics. Here we present cryo-EM structures of human Na V 1.7/β1/β2 complexed with inhibitors XEN907, TC-N1752 and Na V 1.7-IN2, explaining specific binding sites and modulation mechanism for the pore blockers. These inhibitors bind in the central cavity blocking ion permeation, but engage different parts of the cavity wall. XEN907 directly causes α- to π-helix transition of DIV-S6 helix, which tightens the fast inactivation gate. TC-N1752 induces π-helix transition of DII-S6 helix mediated by a conserved asparagine on DIII-S6, which closes the activation gate. Na V 1.7-IN2 serves as a pore blocker without causing conformational change. Electrophysiological results demonstrate that XEN907 and TC-N1752 stabilize Na V 1.7 in inactivated state and delay the recovery from inactivation. Our results provide structural framework for Na V 1.7 modulation by pore blockers, and important implications for developing subtype-selective analgesics.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China. jiangdh@iphy.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent proteinA2,250Homo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 1 
Gene Names: SCN9ANENAgfp
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens)
Explore Q15858 
Go to UniProtKB:  Q15858
PHAROS:  Q15858
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UniProt GroupQ15858
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel subunit beta-1,Green fluorescent proteinB481Homo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: SCN1Bgfp
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07699 (Homo sapiens)
Explore Q07699 
Go to UniProtKB:  Q07699
PHAROS:  Q07699
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UniProt GroupQ07699
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel subunit beta-2C215Homo 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
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UniProt GroupO60939
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, E 2N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G2W (Subject of Investigation/LOI)
Query on G2W

Download Ideal Coordinates CCD File 
H [auth A]3-[[4-[3-(4-fluoranyl-2-methyl-phenoxy)azetidin-1-yl]pyrimidin-2-yl]amino]-~{N}-methyl-benzamide
C22 H22 F N5 O2
MFAKJGXMORSMIX-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
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: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971134

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-28
    Changes: Database references