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- PDB-1mvj: N-TYPE CALCIUM CHANNEL BLOCKER, OMEGA-CONOTOXIN MVIIA NMR, 15 STR... -

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Basic information

Entry
Database: PDB / ID: 1mvj
TitleN-TYPE CALCIUM CHANNEL BLOCKER, OMEGA-CONOTOXIN MVIIA NMR, 15 STRUCTURES
ComponentsSVIB
KeywordsNEUROTOXIN / CONUS STRIATUS PEPTIDE SPECIFIC TO P/Q-TYPE VOLTAGE SENSITIVE CALCIUM CHANNEL
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Conotoxin / Conotoxin
Similarity search - Domain/homology
Omega-conotoxin SVIB
Similarity search - Component
Biological speciesConus striatus (striated cone)
MethodSOLUTION NMR / MD, SIMULATED ANNEALING
AuthorsNielsen, K.J. / Thomas, L. / Lewis, R.J. / Alewood, P.F. / Craik, D.J.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: A consensus structure for omega-conotoxins with different selectivities for voltage-sensitive calcium channel subtypes: comparison of MVIIA, SVIB and SNX-202.
Authors: Nielsen, K.J. / Thomas, L. / Lewis, R.J. / Alewood, P.F. / Craik, D.J.
History
DepositionAug 2, 1996Processing site: BNL
Revision 1.0Aug 12, 1997Provider: 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SVIB


Theoretical massNumber of molelcules
Total (without water)2,7501
Polymers2,7501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50LOW E AND FEW VIOLATIONS OF EXPERIMENTAL RESTRAINTS
Representative

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Components

#1: Protein/peptide SVIB / OMEGA-CONOTOXIN SVIB


Mass: 2750.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus striatus (striated cone) / References: UniProt: P28881
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141E-COSY

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Sample preparation

Sample conditionspH: 3 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: MD, SIMULATED ANNEALING / Software ordinal: 1
Details: CHARM22 A TOTAL OF 50 INITIAL STRUCTURES WERE CALCULATED USING A SIMULATED ANNEALING PROGRAM AS SUPPLIED WITH X-PLOR 3.1. THE FINAL 20 STRUCTURES WITH THE LOWEST OVERALL ENERGIES AND FEWEST ...Details: CHARM22 A TOTAL OF 50 INITIAL STRUCTURES WERE CALCULATED USING A SIMULATED ANNEALING PROGRAM AS SUPPLIED WITH X-PLOR 3.1. THE FINAL 20 STRUCTURES WITH THE LOWEST OVERALL ENERGIES AND FEWEST VIOLATIONS OF NOE AND DIHEDRAL RESTRAINTS WERE ENERGY MINIMIZED IN X-PLOR USING THE CHARMM FORCEFIELD [BROOKS ET AL. (1983) J. COMPUT. CHEM., VOL. 4 187-217.]
NMR ensembleConformer selection criteria: LOW E AND FEW VIOLATIONS OF EXPERIMENTAL RESTRAINTS
Conformers calculated total number: 50 / Conformers submitted total number: 15

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