6J8E

Human Nav1.2-beta2-KIIIA ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 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

Molecular basis for pore blockade of human Na+channel Nav1.2 by the mu-conotoxin KIIIA.

Pan, X.Li, Z.Huang, X.Huang, G.Gao, S.Shen, H.Liu, L.Lei, J.Yan, N.

(2019) Science 363: 1309-1313

  • DOI: 10.1126/science.aaw2999

  • PubMed Abstract: 
  • The voltage-gated sodium channel Na <sub>v </sub>1.2 is responsible for the initiation and propagation of action potentials in the central nervous system. We report the cryo-electron microscopy structure of human Na <sub>v </sub>1.2 bound to a peptid ...

    The voltage-gated sodium channel Na v 1.2 is responsible for the initiation and propagation of action potentials in the central nervous system. We report the cryo-electron microscopy structure of human Na v 1.2 bound to a peptidic pore blocker, the μ-conotoxin KIIIA, in the presence of an auxiliary subunit, β2, to an overall resolution of 3.0 angstroms. The immunoglobulin domain of β2 interacts with the shoulder of the pore domain through a disulfide bond. The 16-residue KIIIA interacts with the extracellular segments in repeats I to III, placing Lys 7 at the entrance to the selectivity filter. Many interacting residues are specific to Na v 1.2, revealing a molecular basis for KIIIA specificity. The structure establishes a framework for the rational design of subtype-specific blockers for Na v channels.


    Organizational Affiliation

    Department of Chemistry, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. nyan@princeton.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium channel subunit beta-2
C
122Homo sapiensMutation(s): 0 
Gene Names: SCN2B
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.4-β2 subunit with bound μ-conotoxin KIIIA
Find proteins for O60939 (Homo sapiens)
Go to Gene View: SCN2B
Go to UniProtKB:  O60939
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium channel protein type 2 subunit alpha
A
2048Homo sapiensMutation(s): 0 
Gene Names: SCN2A (NAC2, SCN2A1, SCN2A2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.4-β2 subunit with bound μ-conotoxin KIIIA
Find proteins for Q99250 (Homo sapiens)
Go to Gene View: SCN2A
Go to UniProtKB:  Q99250
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mu-conotoxin KIIIA
D
16Conus kinoshitaiMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.4-β2 subunit with bound μ-conotoxin KIIIA
Find proteins for P0C195 (Conus kinoshitai)
Go to UniProtKB:  P0C195
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
9Z9
Query on 9Z9

Download SDF File 
Download CCD File 
A
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0500402
Ministry of Science and Technology (China)China2017YFA0505200
Ministry of Science and Technology (China)China2015CB910101
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31630017
National Natural Science Foundation of ChinaChina81861138009
National Natural Science Foundation of ChinaChina91753205
National Natural Science Foundation of ChinaChina31800628

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references