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- PDB-5vnt: Solution NMR Structure of the C-terminal Headpiece Domain of Vill... -

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Basic information

Entry
Database: PDB / ID: 5vnt
TitleSolution NMR Structure of the C-terminal Headpiece Domain of Villin 4 from A.thaliana, the First Non-Vertebrate Headpiece Structure
ComponentsVillin-4Villin-1
KeywordsPROTEIN BINDING / villin / headpiece
Function / homology
Function and homology information


cytoplasmic streaming / root hair elongation / response to abscisic acid / actin filament severing / actin filament capping / actin filament depolymerization / actin filament organization / actin filament binding / cytoskeleton / mRNA binding ...cytoplasmic streaming / root hair elongation / response to abscisic acid / actin filament severing / actin filament capping / actin filament depolymerization / actin filament organization / actin filament binding / cytoskeleton / mRNA binding / plasma membrane / cytosol
Similarity search - Function
Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain ...Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / molecular dynamics
AuthorsMiears, H.L. / Smirnov, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
WWURSP Pilot Project United States
CitationJournal: Biochemistry / Year: 2018
Title: Plant Villin Headpiece Domain Demonstrates a Novel Surface Charge Pattern and High Affinity for F-Actin.
Authors: Miears, H.L. / Gruber, D.R. / Horvath, N.M. / Antos, J.M. / Young, J. / Sigurjonsson, J.P. / Klem, M.L. / Rosenkranz, E.A. / Okon, M. / McKnight, C.J. / Vugmeyster, L. / Smirnov, S.L.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Villin-4


Theoretical massNumber of molelcules
Total (without water)7,5011
Polymers7,5011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Villin-4 / Villin-1


Mass: 7500.623 Da / Num. of mol.: 1 / Fragment: unp residues 921-983
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VLN4, At4g30160, F6G3.190, F9N11.10 / Production host: Escherichia coli (E. coli) / References: UniProt: O65570

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic115N-HSQC
123isotropic213C-HSQC
133isotropic33D HN(CA)CB
143isotropic33D CBCA(CO)NH
153isotropic33D HNCO
163isotropic33D HN(CA)CO
173isotropic33D 1H-15N NOESY
183isotropic33D 1H-13C NOESY aliphatic
193isotropic33D 1H-13C NOESY aromatic
1103isotropic33D C(CO)NH
1113isotropic33D HCC(CO)NH
1123isotropic33D HBHA(CO)NH
1133isotropic22D (HB)CB(CGCD)HD

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution31.0 mM atVHP, 20.0 mM PIPES, 50 mM sodium chloride, 0.01 % sodium azide, 90% H2O/10% D2O13C/15N-atVHP7690% H2O/10% D2O
solution51.0 mM atVHP, 20.0 mM PIPES, 50 mM sodium chloride, 0.01 % sodium azide, 90% H2O/10% D2OatVHP76 unlabled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMatVHPnone3
20.0 mMPIPESnone3
50 mMsodium chloridenone3
0.01 %sodium azidenone3
1.0 mMatVHPnone5
20.0 mMPIPESnone5
50 mMsodium chloridenone5
0.01 %sodium azidenone5
Sample conditionsIonic strength: 50 mM / Label: Standard buffer / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III5001TCI probe
Bruker AVANCE IIIBrukerAVANCE III6002TCI probe
Bruker AVANCE IIIBrukerAVANCE III8503TCI probe

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.1Bruker Biospincollection
NMRView9Johnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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