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- PDB-2d8b: Solution structure of the second tandem cofilin-domain of mouse t... -

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Basic information

Entry
Database: PDB / ID: 2d8b
TitleSolution structure of the second tandem cofilin-domain of mouse twinfilin
ComponentsTwinfilin-1
KeywordsPROTEIN BINDING / cell-free protein synthesis / actin-binding protein / developmental regulation / cellular remodeling / cytoskeleton / morphology / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / actin filament depolymerization / barbed-end actin filament capping / regulation of lamellipodium assembly / myofibril / positive regulation of cardiac muscle hypertrophy / actin monomer binding ...: / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / actin filament depolymerization / barbed-end actin filament capping / regulation of lamellipodium assembly / myofibril / positive regulation of cardiac muscle hypertrophy / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / filopodium / actin filament / positive regulation of neuron projection development / actin filament binding / cell-cell junction / actin cytoskeleton / protein tyrosine kinase activity / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Twinfilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Kigawa, T. / Koshiba, S. / Sato, M. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2009
Title: NMR solution structures of actin depolymerizing factor homology domains
Authors: Goroncy, A.K. / Koshiba, S. / Tochio, N. / Tomizawa, T. / Sato, M. / Inoue, M. / Watanabe, S. / Hayashizaki, Y. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4May 29, 2024Group: 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: Twinfilin-1


Theoretical massNumber of molelcules
Total (without water)18,8891
Polymers18,8891
Non-polymers00
Water00
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Twinfilin-1 / Twinfilin / A6 protein / Protein tyrosine kinase 9


Mass: 18889.189 Da / Num. of mol.: 1 / Fragment: COFILIN HOMOLOGY DOMAIN, UNP Residues 161-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptk9 / Plasmid: P050302-01 / Production host: CELL-FREE PROTEIN SYNTHESIS / References: UniProt: Q91YR1

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.44mM COFILIN HOMOLOGY DOMAIN, 20mM d-Tris-HCL, 100mM NaCl, 1mM d-DTT, 0.02 % NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERcollection
NMRPipe20020425FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.899aNAOHIRO KOBAYASHIdata analysis
CYANA2.2.1PETER GUNTERT ET AL.refinement
CYANA2.2.1PETER GUNTERT ET AL.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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