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- PDB-25ij: Cryo-EM structure of human Nav1.6 in complex with delta-paraponer... -

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Basic information

Entry
Database: PDB / ID: 25ij
TitleCryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a
Components
  • (Sodium channel ...) x 2
  • Delta-paraponeritoxin-Pc1a
KeywordsMEMBRANE PROTEIN / Nav1.6 / voltage gated sodium channel / toxin / Pc1a / delta-paraponeritoxin-Pc1a / TRANSPORT PROTEIN
Function / homology
Function and homology information


corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / host cell postsynaptic membrane / regulation of atrial cardiac muscle cell membrane depolarization / sodium ion binding / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport ...corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / host cell postsynaptic membrane / regulation of atrial cardiac muscle cell membrane depolarization / sodium ion binding / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport / peripheral nervous system development / regulation of sodium ion transmembrane transport / axon initial segment / regulation of ventricular cardiac muscle cell membrane repolarization / node of Ranvier / cardiac muscle cell action potential involved in contraction / host cell presynaptic membrane / sodium channel inhibitor activity / voltage-gated sodium channel complex / podosome / neuronal action potential propagation / locomotion / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / intercalated disc / action potential / sodium channel regulator activity / membrane depolarization / cardiac muscle contraction / myelination / T-tubule / axon guidance / sodium ion transmembrane transport / positive regulation of neuron projection development / Z disc / Sensory perception of sweet, bitter, and umami (glutamate) taste / cell junction / toxin activity / cytoplasmic vesicle / perikaryon / transmembrane transporter binding / cell adhesion / axon / extracellular region / membrane / plasma membrane
Similarity search - Function
Voltage gated sodium channel, alpha-8 subunit / Sodium channel subunit beta-1/beta-3 / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / : / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit ...Voltage gated sodium channel, alpha-8 subunit / Sodium channel subunit beta-1/beta-3 / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / : / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Voltage-dependent channel domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ion transport domain / Ion transport protein / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / CHOLESTEROL HEMISUCCINATE / Glycyl-poneratoxin / Sodium channel regulatory subunit beta-1 / Sodium channel protein type 8 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Paraponera clavata (insect)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYang, L. / Fan, X. / Huang, J. / Yan, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32330052, 32322039, 32271252, and 32501082 China
CitationJournal: To Be Published
Title: Diverse binding poses of gating modifier neurotoxins as agonists of human Nav1.6
Authors: Fan, X. / Jian, H. / Yang, L. / Chen, J. / Wang, H. / Huang, X. / Geng, J. / Wu, Q. / Xie, Y. / Lu, F. / Guo, Q. / Shen, Z. / Jin, X. / Yan, N.
History
DepositionApr 6, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium channel protein type 8 subunit alpha
B: Delta-paraponeritoxin-Pc1a
C: Sodium channel regulatory subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,23215
Polymers248,4843
Non-polymers6,74812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Sodium channel ... , 2 types, 2 molecules AC

#1: Protein Sodium channel protein type 8 subunit alpha / Sodium channel protein type VIII subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.6


Mass: 225520.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN8A, MED / Production host: Homo sapiens (human) / References: UniProt: Q9UQD0
#3: Protein Sodium channel regulatory subunit beta-1


Mass: 20206.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN1B / Production host: Homo sapiens (human) / References: UniProt: Q07699

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Protein/peptide , 1 types, 1 molecules B

#2: Protein/peptide Delta-paraponeritoxin-Pc1a / Delta-PPOTX-Pc1a / Pac-TX / Poneratoxin / PoTX / Poneritoxin


Mass: 2757.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraponera clavata (insect) / Production host: synthetic construct (others) / References: UniProt: P41736

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Sugars , 3 types, 6 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a3-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 6 molecules

#7: Chemical ChemComp-9Z9 / (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en


Mass: 544.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H56O5 / Comment: detergent*YM
#8: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#9: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nav1.6-Pc1a / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Paraponera clavata (insect)55425
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Paraponera clavata (insect)55425
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191257 / Symmetry type: POINT

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