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- PDB-1x67: Solution structure of the cofilin homology domain of HIP-55 (dreb... -

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Basic information

Entry
Database: PDB / ID: 1x67
TitleSolution structure of the cofilin homology domain of HIP-55 (drebrin-like protein)
ComponentsDrebrin-like protein
KeywordsPROTEIN BINDING / cell-free protein synthesis / actin-binding protein / SH3P7 / mAbp1 / T-cell lymphocyte signaling and regulation / T-cell antigen receptor regulation / HPK-1 activation / c-JUN N-terminal kinase activation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


podosome assembly / clathrin-coated vesicle membrane / structural constituent of postsynaptic actin cytoskeleton / membrane organization / podosome / anchoring junction / Neurexins and neuroligins / Rac protein signal transduction / Caspase-mediated cleavage of cytoskeletal proteins / synapse assembly ...podosome assembly / clathrin-coated vesicle membrane / structural constituent of postsynaptic actin cytoskeleton / membrane organization / podosome / anchoring junction / Neurexins and neuroligins / Rac protein signal transduction / Caspase-mediated cleavage of cytoskeletal proteins / synapse assembly / neuron projection morphogenesis / ruffle / enzyme activator activity / endocytosis / actin filament binding / tertiary granule lumen / lamellipodium / presynapse / actin binding / cell cortex / perikaryon / secretory granule lumen / adaptive immune response / ficolin-1-rich granule lumen / early endosome / postsynaptic density / cadherin binding / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / dendrite / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Drebrin-like protein, SH3 domain / 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 / Variant SH3 domain / Src homology 3 domains ...Drebrin-like protein, SH3 domain / 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 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Drebrin-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
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
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 1.4May 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: Drebrin-like protein


Theoretical massNumber of molelcules
Total (without water)15,4031
Polymers15,4031
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 Drebrin-like protein / SH3 domain-containing protein 7 / Drebrin F / Cervical SH3P7 / HPK1-interacting protein of 55 kDa / ...SH3 domain-containing protein 7 / Drebrin F / Cervical SH3P7 / HPK1-interacting protein of 55 kDa / HIP-55 / Cervical mucin-associated protein / PP5423


Mass: 15403.144 Da / Num. of mol.: 1 / Fragment: cofilin homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: DBNL / Plasmid: P041129-01 / References: UniProt: Q9UJU6

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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: 1.33mM COFILIN HOMOLOGY DOMAIN, 20mM TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERcollection
NMRPipe20020425FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.899aNAOHIRO KOBAYASHdata analysis
CYANA2PETER GUNTERTrefinement
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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