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- PDB-6a91: Complex of voltage-gated sodium channel NavPaS from American cock... -

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Basic information

Entry
Database: PDB / ID: 6a91
TitleComplex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with saxitoxin and Dc1a
Components
  • Mu-diguetoxin-Dc1a
  • Sodium channel protein PaFPC1
KeywordsMEMBRANE PROTEIN/TOXIN / complex / sodium channel / toxin / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TOXIN complex
Function / homology
Function and homology information


voltage-gated sodium channel complex / host cell presynaptic membrane / voltage-gated sodium channel activity / sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #120 / Beta/Mu-diguetoxin-1 / Spider Toxins mu-diguetoxin-1 a, b and c / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain ...Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #120 / Beta/Mu-diguetoxin-1 / Spider Toxins mu-diguetoxin-1 a, b and c / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-9SL / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sodium channel protein PaFPC1 / Beta-diguetoxin-Dc1a
Similarity search - Component
Biological speciesPeriplaneta americana (American cockroach)
Diguetia canities (spider)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShen, H.Z. / li, Z.Q. / Jiang, Y. / Pan, X.J. / Wu, J.P. / Cristofori-Armstrong, B. / Smith, J.J. / Chin, Y.K.Y. / Lei, J.L. / Zhou, Q. ...Shen, H.Z. / li, Z.Q. / Jiang, Y. / Pan, X.J. / Wu, J.P. / Cristofori-Armstrong, B. / Smith, J.J. / Chin, Y.K.Y. / Lei, J.L. / Zhou, Q. / King, G.F. / Yan, N.
Funding support China, Australia, 7items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2015CB910101 China
Ministry of Science and Technology (China)2016YFA0500402 China
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31630017 China
National Natural Science Foundation of China31611130036 China
Australian Research CouncilDP160104411 Australia
National Health and Medical Research Council (Australia)APP1072113 Australia
CitationJournal: Science / Year: 2018
Title: Structural basis for the modulation of voltage-gated sodium channels by animal toxins.
Authors: Huaizong Shen / Zhangqiang Li / Yan Jiang / Xiaojing Pan / Jianping Wu / Ben Cristofori-Armstrong / Jennifer J Smith / Yanni K Y Chin / Jianlin Lei / Qiang Zhou / Glenn F King / Nieng Yan /
Abstract: Animal toxins that modulate the activity of voltage-gated sodium (Na) channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and ...Animal toxins that modulate the activity of voltage-gated sodium (Na) channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and saxitoxin (STX) are responsible for puffer fish and shellfish poisoning in humans, respectively. Here, we present structures of the insect Na channel NaPaS bound to a gating modifier toxin Dc1a at 2.8 angstrom-resolution and in the presence of TTX or STX at 2.6-Å and 3.2-Å resolution, respectively. Dc1a inserts into the cleft between VSD and the pore of NaPaS, making key contacts with both domains. The structures with bound TTX or STX reveal the molecular details for the specific blockade of Na access to the selectivity filter from the extracellular side by these guanidinium toxins. The structures shed light on structure-based development of Na channel drugs.
History
DepositionJul 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

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Assembly

Deposited unit
A: Sodium channel protein PaFPC1
B: Mu-diguetoxin-Dc1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,77010
Polymers190,3782
Non-polymers3,3928
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5770 Å2
ΔGint-7 kcal/mol
Surface area72780 Å2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Sodium channel protein PaFPC1 / / Voltage-gated sodium channel / PaFPC1 / NavPaS


Mass: 183875.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Periplaneta americana (American cockroach)
Production host: Homo sapiens (human) / References: UniProt: D0E0C2
#2: Protein Mu-diguetoxin-Dc1a / Mu-DGTX-Dc1a / Insecticidal toxin DTX9.2


Mass: 6502.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diguetia canities (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P49126

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Sugars , 2 types, 5 molecules

#3: 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.: 2 / Source method: obtained synthetically
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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / 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

#5: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C44H88NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-9SL / [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate / Saxitoxin / Saxitoxin


Mass: 299.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N7O4 / Comment: neurotoxin*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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

Component
IDNameTypeEntity IDParent-IDSource
1complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with saxitoxin and Dc1aCOMPLEX#1-#20RECOMBINANT
2voltage-gated sodium channel NavPaS from American cockroach Periplaneta americanaCOMPLEX#11RECOMBINANT
3Dc1aCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Periplaneta americana (American cockroach)6978
23Diguetia canities (spider)38407
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Escherichia coli (E. coli)562
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166805 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811285
ELECTRON MICROSCOPYf_angle_d1.06115347
ELECTRON MICROSCOPYf_dihedral_angle_d12.0256540
ELECTRON MICROSCOPYf_chiral_restr0.0591740
ELECTRON MICROSCOPYf_plane_restr0.0071901

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