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- PDB-8f04: Structure of elevenin-Vc1 from venom of the Australian cone snail... -

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Basic information

Entry
Database: PDB / ID: 8f04
TitleStructure of elevenin-Vc1 from venom of the Australian cone snail Conus victoriae
ComponentsElevenin-Vc1
KeywordsHORMONE / Venom / Hormone-like
Function / homologytoxin activity / extracellular region / Elevenin-Vc1
Function and homology information
Biological speciesConus victoriae (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsKrishnarjuna, B. / Sunanda, P. / Norton, R.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Mar Drugs / Year: 2023
Title: Characterisation of Elevenin-Vc1 from the Venom of Conus victoriae : A Structural Analogue of alpha-Conotoxins.
Authors: Krishnarjuna, B. / Sunanda, P. / Seow, J. / Tae, H.S. / Robinson, S.D. / Belgi, A. / Robinson, A.J. / Safavi-Hemami, H. / Adams, D.J. / Norton, R.S.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elevenin-Vc1


Theoretical massNumber of molelcules
Total (without water)2,1261
Polymers2,1261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Elevenin-Vc1


Mass: 2125.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus victoriae (invertebrata) / References: UniProt: A0A0F7YZQ7
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
111isotropic11D proton
121isotropic12D DQF-COSY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.8 mM Elevenin-Cv1, 95% H2O/5% D2O / Details: 0.8 mM in water, pH 4.5 / Label: Elevenin-Cv1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: Elevenin-Cv1 / Isotopic labeling: natural abundance
Sample conditionsDetails: 0.8 mM in water, pH 4.5 / Ionic strength: NA Not defined / Label: Elevenin-Cv1 / pH: 4.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance 600 / Manufacturer: Bruker / Model: Avance 600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
TopSpinBruker Biospindata analysis
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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