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- PDB-2hd7: Solution structure of C-teminal domain of twinfilin-1. -

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Basic information

Entry
Database: PDB / ID: 2hd7
TitleSolution structure of C-teminal domain of twinfilin-1.
ComponentsTwinfilin-1
KeywordsCONTRACTILE PROTEIN / ADF-H / Actin binding protein
Function / homology
Function and homology information


regulation of actin phosphorylation / 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 ...regulation of actin phosphorylation / 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 / cell-cell junction / actin filament binding / actin cytoskeleton / protein tyrosine kinase activity / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / cytoplasm / cytosol
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, simulated annealing
AuthorsHellman, M.H. / Paavilainen, V.O. / Annila, A. / Lappalainen, P. / Permi, P.I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis and evolutionary origin of actin filament capping by twinfilin
Authors: Paavilainen, V.O. / Hellman, M. / Helfer, E. / Bovellan, M. / Annila, A. / Carlier, M.F. / Permi, P. / Lappalainen, P.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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_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 / _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)16,6391
Polymers16,6391
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)15 / 40structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Twinfilin-1 / Protein A6


Mass: 16638.953 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 176-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptk9 / Plasmid: pRat4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q91YR1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N-HSQC
12113C-HSQC
13113C-(CT)-HSQC
1413D HNCA
151HN(CO)CA
161HN(CA)CB
171CBCA(CO)NH
181HNCO, HN(CA)CO
191HC(C)H-COSY
1101H(C)CH-TOCSY
1111H)C(CO)NH
1121H(C)(CO)NH
1131(HB)CB(CGCDCE)HE
1141HB)CB(CGCD)HD
1151NOESY-15N-HSQC
1161NOESY-13C-HSQC

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Sample preparation

DetailsContents: 1 mM C-terminal domain of twinfilin U-15N, C13, 10 mM Bis-Tris, pH 6.8, 50 mM NaCl, 1 mM DTT, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 60 / pH: 6.8 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Cprocessing
Sparky3.11Goddard, T.D. and Kneller, D.G.data analysis
CYANA2.1Guntert, P., Mumenthaler, C., and Wuthrich, K.structure solution
Amber8Case, D.A.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 15

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