6J8E

Human Nav1.2-beta2-KIIIA ternary complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    6J8E

  • PubMed Abstract: 

    • 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 ...

    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: 

    Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel subunit beta-2A [auth C]122Homo sapiensMutation(s): 0 
Gene Names: SCN2B, UNQ326/PRO386
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O60939 (Homo sapiens)
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Go to UniProtKB:  O60939
PHAROS:  O60939
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UniProt GroupO60939
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel protein type 2 subunit alphaB [auth A]2,048Homo sapiensMutation(s): 0 
Gene Names: SCN2A, NAC2, SCN2A1, SCN2A2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99250 (Homo sapiens)
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Go to UniProtKB:  Q99250
PHAROS:  Q99250
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UniProt GroupQ99250
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mu-conotoxin KIIIAC [auth D]16Conus kinoshitaiMutation(s): 0 
UniProt
Find proteins for P0C195 (Conus kinoshitai)
Explore P0C195 
Go to UniProtKB:  P0C195
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UniProt GroupP0C195
Protein Feature View
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Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9Z9
Query on 9Z9
Download Ideal Coordinates CCD File 
H [auth A](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N		 Ligand Interaction
NAG
Query on NAG
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G [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
NA
Query on NA
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I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary