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- PDB-1vtx: DELTA-ATRACOTOXIN-HV1 (VERSUTOXIN) FROM HADRONYCHE VERSUTA, NMR, ... -

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Basic information

Entry
Database: PDB / ID: 1vtx
TitleDELTA-ATRACOTOXIN-HV1 (VERSUTOXIN) FROM HADRONYCHE VERSUTA, NMR, 20 STRUCTURES
ComponentsDELTA-ATRACOTOXIN-HV1
KeywordsNEUROTOXIN / SODIUM CHANNEL TOXIN / CYSTEINE KNOT / VENOM
Function / homology
Function and homology information


sodium channel inhibitor activity / toxin activity / extracellular region
Similarity search - Function
Atracotoxin, delta / Delta Atracotoxin / Delta-atracotoxin (ACTX) family signature. / Omega-AgatoxinV - #10 / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Delta-hexatoxin-Hv1a
Similarity search - Component
Biological speciesHadronyche versuta (spider)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING
AuthorsFletcher, J.I. / Chapman, B.E. / King, G.F.
Citation
Journal: Structure / Year: 1997
Title: The structure of versutoxin (delta-atracotoxin-Hv1) provides insights into the binding of site 3 neurotoxins to the voltage-gated sodium channel.
Authors: Fletcher, J.I. / Chapman, B.E. / Mackay, J.P. / Howden, M.E. / King, G.F.
#1: Journal: Toxicon / Year: 1996
Title: Selective Alteration of Sodium Channel Gating by Australian Funnel-Web Spider Toxins
Authors: Nicholson, G.M. / Little, M.J. / Tyler, M. / Narahashi, T.
#2: Journal: Biochem.J. / Year: 1989
Title: Erratum. Amino Acid Sequence of Versutoxin, a Lethal Neurotoxin from the Venom of the Funnel-Web Spider Atrax Versutus
Authors: Brown, M.R. / Sheumack, D.D. / Tyler, M.I. / Howden, M.E.
#3: Journal: Biochem.J. / Year: 1988
Title: Amino Acid Sequence of Versutoxin, a Lethal Neurotoxin from the Venom of the Funnel-Web Spider Atrax Versutus
Authors: Brown, M.R. / Sheumack, D.D. / Tyler, M.I. / Howden, M.E.
History
DepositionMar 13, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DELTA-ATRACOTOXIN-HV1


Theoretical massNumber of molelcules
Total (without water)4,8631
Polymers4,8631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 75LOWEST ENERGY
Representative

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Components

#1: Protein/peptide DELTA-ATRACOTOXIN-HV1 / VERSUTOXIN


Mass: 4862.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hadronyche versuta (spider) / Secretion: VENOM / References: UniProt: P13494
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQFCOSY
131TOCSY
141ECOSY

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Sample preparation

Sample conditionspH: 2.6 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX500BrukerDRX5005001
Bruker AMX600BrukerAMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DIANAstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: SEE PRIMARY REFERENCE ABOVE. OTHER PROGRAM USED DIANA VERSION 2.8 BY GUNTERT.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 75 / Conformers submitted total number: 20

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