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- PDB-6vy7: Structural characterization of novel conotoxin MIIIB derived from... -

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Basic information

Entry
Database: PDB / ID: 6vy7
TitleStructural characterization of novel conotoxin MIIIB derived from Conus magus
ComponentsConotoxin MIIIB
KeywordsTOXIN / venom peptide
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / extracellular region / Conotoxin superfamily M
Function and homology information
Biological speciesConus magus (magus cone)
MethodSOLUTION NMR / simulated annealing
AuthorsLoening, N.M.
Funding support United States, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)HATCH HAW00595-R United States
United States Department of Agriculture (USDA)NIFA # 2011-37610-31182 United States
CitationJournal: To Be Published
Title: Discovery and characterization of novel conotoxin MIIIB derived from Conus magus: The expansion of conotoxin diversity
Authors: Zhang, R.-Y. / Espirtu, M.J. / Loening, N.M. / Kapono, C.A. / Bingham, J.-P.
History
DepositionFeb 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Nov 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conotoxin MIIIB


Theoretical massNumber of molelcules
Total (without water)2,4581
Polymers2,4581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area1950 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Conotoxin MIIIB


Mass: 2457.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus magus (magus cone) / References: UniProt: A0A679PEX4*PLUS
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 2 mM MIIIB Isomer F, 0.5 mM DSS, 95% H2O/5% D2O
Details: Synthetically produced MIIIB purified by prep RP-HPLC and analytical RP-HPLC to isolate isomer F, which has the disulfide connectivity C1-C6, C2-C4, C3-C5.
Label: MIIIB_Isomer_F / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMMIIIB Isomer Fnatural abundance1
0.5 mMDSSnatural abundance1
Sample conditionsDetails: Sample prepared by dissolving lyophilized peptide in 95% H2O/5% D2O with 0.5 mM DSS, pH was adjusted to 3.8 using dropwise addition of 500 mM hydrochloric acid.
Ionic strength: 0 mM / Label: conditions_1 / pH: 3.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz / Details: TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: log harmonic potential used, water refinement used for 20 lowest energy structure
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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