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- PDB-1ryv: Three dimensional solution structure of the K27A MUTANT of sodium... -

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Basic information

Entry
Database: PDB / ID: 1ryv
TitleThree dimensional solution structure of the K27A MUTANT of sodium channels inhibitor HAINANTOXIN-IV BY 2D 1H-NMR
ComponentsHainantoxin-IV
KeywordsTOXIN / NEUROTOXIN / INHIBITOR CYSTINE KNOT MOTIF
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Huwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
Mu-theraphotoxin-Hhn1b 1 / Mu-theraphotoxin-Hhn1b 1
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsLi, D. / Lu, S. / Gu, X. / Liang, S.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structure--activity relationships of hainantoxin-IV and structure determination of active and inactive sodium channel blockers
Authors: Li, D. / Xiao, Y. / Xu, X. / Xiong, X. / Lu, S. / Liu, Z. / Zhu, Q. / Wang, M. / Gu, X. / Liang, S.
#1: Journal: Acta Biochim.Biophys.Sinica / Year: 2002
Title: Synthesis and Oxidative Refolding of Hainantoxin-Iv
Authors: Liu, Z.H. / Chen, P. / Liang, S.P.
#2: Journal: Cell.Mol.Life Sci. / Year: 2003
Title: Isolation and characterization of hainantoxin-IV, a novel antagonist of tetrodotoxin-sensitive sodium channels from the Chinese bird spider Selenocosmia hainana
Authors: Liu, Z. / Dai, J. / Chen, Z. / Hu, W. / Xiao, Y. / Liang, S.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hainantoxin-IV


Theoretical massNumber of molelcules
Total (without water)3,9421
Polymers3,9421
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Hainantoxin-IV / HnTx-IV


Mass: 3941.527 Da / Num. of mol.: 1 / Mutation: K27A / Source method: obtained synthetically / Details: synthesized using standard fmoc chemistry. / References: UniProt: P83471, UniProt: D2Y232*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
NMR detailsText: this structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5.0mM
Solvent system: 20mM deuterium acetic acid BU, 90% H2O, 10% D2O
Sample conditionsIonic strength: 20 / pH: 4 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionClassification
X-PLOR3.851refinement
Felix98structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 378 NOE-derived distance constraints, 13 dihedral angle restraints, 9 fake distance restraints from disulfide bonds and 12 hydrogen-bond constrains.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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