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- PDB-2jm0: Solution structure of chicken villin headpiece subdomain containi... -

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Basic information

Entry
Database: PDB / ID: 2jm0
TitleSolution structure of chicken villin headpiece subdomain containing a fluorinated side chain in the core
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / fluorinated Phe / VHP / chicken villin headpiece
Function / homology
Function and homology information


regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / microvillus / cellular response to epidermal growth factor stimulus / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / regulation of cell shape / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsCornilescu, C.C. / Cornilescu, G. / Hadley, E.B. / Gellman, S.H. / Markley, J.L.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure of a small protein containing a fluorinated side chain in the core.
Authors: Cornilescu, G. / Hadley, E.B. / Woll, M.G. / Markley, J.L. / Gellman, S.H. / Cornilescu, C.C.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Villin-1


Theoretical massNumber of molelcules
Total (without water)4,2951
Polymers4,2951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Villin-1


Mass: 4294.729 Da / Num. of mol.: 1 / Fragment: residues 792-826 / Source method: obtained synthetically
Details: This sequence occurs naturally in Gallus gallus (Chicken).
References: UniProt: P02640

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D COSY
1412D TOCSY
1512D NOESY
1622D 1H-15N HSQC
1722D HNCO
1822D HN(CA)CB
1922D HNHA
11022D HNHB
111119F-HOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM F5-Phe-cVHP93% H2O/7% D2O
22 mM selectively 15N-[Ala, Phe, Leu] F5-Phe-cVHP93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMF5-Phe-cVHPnatural abundance1
2 mMF5-Phe-cVHPselectively 15N-[Ala, Phe, Leu]2
Sample conditionsIonic strength: 10 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503
Varian INOVAVarianINOVA6004
Varian INOVAVarianINOVA8005
Varian INOVAVarianINOVA9006

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
PIPPGarrett, D.data analysis
SparkyGoddard, T.data analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.structure solution
X-PLOR NIHSchwieters, C.D. et al.structure solution
X-PLOR NIHSchwieters, C.D. et al.refinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
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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