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- PDB-1bmr: ALPHA-LIKE TOXIN LQH III FROM SCORPION LEIURUS QUINQUESTRIATUS HE... -

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Entry
Database: PDB / ID: 1bmr
TitleALPHA-LIKE TOXIN LQH III FROM SCORPION LEIURUS QUINQUESTRIATUS HEBRAEUS, NMR, 25 STRUCTURES
ComponentsLQH III ALPHA-LIKE TOXIN
KeywordsTOXIN / ALPHA-LIKE TOXIN / SCORPION TOXIN / SODIUM CHANNEL INHIBITOR
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-like toxin Lqh3
Similarity search - Component
Biological speciesLeiurus quinquestriatus hebraeus (scorpion)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsKrimm, I. / Gilles, N. / Sautiere, P. / Stankiewicz, M. / Pelhate, M. / Gordon, D. / Lancelin, J.-M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: NMR structures and activity of a novel alpha-like toxin from the scorpion Leiurus quinquestriatus hebraeus.
Authors: Krimm, I. / Gilles, N. / Sautiere, P. / Stankiewicz, M. / Pelhate, M. / Gordon, D. / Lancelin, J.M.
#1: Journal: Toxicon / Year: 1998
Title: New Toxins Acting on Sodium Channels from the Scorpion Leiurus Quinquestriatus Hebraeus Suggest a Clue to Mammalian Vs Insect Selectivity
Authors: Sautiere, P. / Cestele, S. / Kopeyan, C. / Martinage, A. / Drobecq, H. / Doljansky, Y. / Gordon, D.
#2: Journal: Toxins and Signal Transduction (in: Cellular and Molecular Mechanisms of Toxin Action, V.1)
Year: 1997
Title: Sodium Channels as Targets for Neurotoxins. Modes of Action and Interaction of Neurotoxins with Receptor Sites on Sodium Channels
Authors: Gordon, D.
History
DepositionJul 24, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: LQH III ALPHA-LIKE TOXIN


Theoretical massNumber of molelcules
Total (without water)7,0641
Polymers7,0641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 60LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein LQH III ALPHA-LIKE TOXIN


Mass: 7063.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AMIDATED AT THE C-TERMINAL POSITION (CONH2) . THIS STRUCTURE IS IN EQUILIBRIUM WITH THE PRO9-GLU10 CIS ISOMER (PDB:1FH3).
Source: (natural) Leiurus quinquestriatus hebraeus (scorpion)
Organ: VENOMOUS APPARATUS / Secretion: VENOM / Species: Leiurus quinquestriatus / Strain: hebraeus / References: UniProt: P56678
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: DQF-COSY TOCSY/HOHAHA NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TWO-DIMENSIONAL NMR ON A NATURAL UNLABELLED SAMPLE OF LQH III ALPHA LIKE TOXIN FROM THE SCORPION LEIURUS QUINQUESTRIATUS HEBRAEUS VENOM.

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 100 mM PHOSPHATE BUFFER / pH: 5.8 / Pressure: 1 atm / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX500 / Manufacturer: Bruker / Model: AVANCE DRX500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Gifa4.2structure solution
BRUKER XWINNMRXWINNMRstructure solution
X-PLOR3.851structure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 60 / Conformers submitted total number: 25

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