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- PDB-1ujs: Solution structure of the Villin headpiece domain of human actin-... -

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Basic information

Entry
Database: PDB / ID: 1ujs
TitleSolution structure of the Villin headpiece domain of human actin-binding LIM protein homologue (KIAA0843 protein)
Componentsactin-binding LIM protein homologue
KeywordsSTRUCTURAL PROTEIN / VHP domain / actin binding / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DCC mediated attractive signaling / positive regulation of protein targeting to mitochondrion / lamellipodium assembly / cilium assembly / stress fiber / cytoskeleton organization / actin filament binding / actin cytoskeleton / lamellipodium / transcription by RNA polymerase II ...DCC mediated attractive signaling / positive regulation of protein targeting to mitochondrion / lamellipodium assembly / cilium assembly / stress fiber / cytoskeleton organization / actin filament binding / actin cytoskeleton / lamellipodium / transcription by RNA polymerase II / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm
Similarity search - Function
Putative adherens-junction anchoring domain / Putative adherens-junction anchoring region of AbLIM / Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / LIM zinc-binding domain signature. ...Putative adherens-junction anchoring domain / Putative adherens-junction anchoring region of AbLIM / Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Actin-binding LIM protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Villin headpiece domain of human actin-binding LIM protein homologue (KIAA0843 protein)
Authors: Tochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionAug 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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_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_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: actin-binding LIM protein homologue


Theoretical massNumber of molelcules
Total (without water)10,2441
Polymers10,2441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein actin-binding LIM protein homologue / KIAA0843 protein


Mass: 10243.581 Da / Num. of mol.: 1 / Fragment: VHP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA hk05155 / Plasmid: P020930-61 / References: UniProt: O94929

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.2mM VHP domain U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe200204025Delaglio, Fprocessing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.816Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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