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- PDB-6dz9: Solution structure of Rbfox2 RRM mimetic peptide CPfox2 -

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Basic information

Entry
Database: PDB / ID: 6dz9
TitleSolution structure of Rbfox2 RRM mimetic peptide CPfox2
ComponentsCPfox2
KeywordsRNA BINDING PROTEIN / peptidomimetics / peptide structure / RNA recognition
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsSun, Y.-T. / Shortridge, M.D. / Varani, G.
CitationJournal: Chembiochem / Year: 2019
Title: A Small Cyclic beta-Hairpin Peptide Mimics the Rbfox2 RNA Recognition Motif and Binds to the Precursor miRNA 20b.
Authors: Sun, Y.T. / Shortridge, M.D. / Varani, G.
History
DepositionJul 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value
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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CPfox2


Theoretical massNumber of molelcules
Total (without water)1,7211
Polymers1,7211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1590 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CPfox2


Mass: 1721.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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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 TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 3.0 mg/mL CPfox2, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.0 mg/mL / Component: CPfox2 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 10 mM potassium phosphate, 10 mM potassium chloride mM
Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 278 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
NameDeveloperClassification
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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