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- PDB-2aav: Solution NMR structure of Filamin A domain 17 -

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Basic information

Entry
Database: PDB / ID: 2aav
TitleSolution NMR structure of Filamin A domain 17
ComponentsFilamin A
KeywordsPROTEIN BINDING / Filamin A Domain 17 / beta-sandwich
Function / homology
Function and homology information


regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / actin crosslink formation / tubulin deacetylation ...regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / actin crosslink formation / tubulin deacetylation / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / Cell-extracellular matrix interactions / early endosome to late endosome transport / Fc-gamma receptor I complex binding / positive regulation of potassium ion transmembrane transport / apical dendrite / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / wound healing, spreading of cells / podosome / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / receptor clustering / positive regulation of axon regeneration / cortical cytoskeleton / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / brush border / semaphorin-plexin signaling pathway / cilium assembly / blood vessel remodeling / mitotic spindle assembly / epithelial to mesenchymal transition / potassium channel regulator activity / axonal growth cone / heart morphogenesis / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / protein sequestering activity / regulation of cell migration / dendritic shaft / protein kinase C binding / protein localization to plasma membrane / actin filament / negative regulation of DNA-binding transcription factor activity / trans-Golgi network / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / establishment of protein localization / synapse organization / negative regulation of protein catabolic process / cerebral cortex development / small GTPase binding / Z disc / kinase binding / platelet aggregation / positive regulation of protein import into nucleus / actin filament binding / cell-cell junction / Platelet degranulation / actin cytoskeleton / negative regulation of neuron projection development / actin cytoskeleton organization / GTPase binding / angiogenesis / DNA-binding transcription factor binding / perikaryon / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / postsynapse / protein stabilization / cadherin binding / focal adhesion / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / The structure calculations were made with the program CYANA 2.0 using the automated NOE assignment, structure calculation algorithm. The structure refinement of the 20 final CYANA structures was made with AMBER 8.0 program using the generalized Born continuum solvent model.
AuthorsNakamura, F. / Pudas, R. / Heikkinen, O. / Permi, P. / Kilpelainen, I. / Munday, A.D. / Hartwig, J.H. / Stossel, T.P. / Ylanne, J.
CitationJournal: Blood / Year: 2006
Title: The structure of the GPIb-filamin A complex
Authors: Nakamura, F. / Pudas, R. / Heikkinen, O. / Permi, P. / Kilpelainen, I. / Munday, A.D. / Hartwig, J.H. / Stossel, T.P. / Ylanne, J.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 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_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: Filamin A


Theoretical massNumber of molelcules
Total (without water)10,0751
Polymers10,0751
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 / 300structures with favorable non-bond energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Filamin A / Alpha-filamin / Filamin 1 / Endothelial actin-binding protein / Actin-binding protein 280 / ABP-280 ...Alpha-filamin / Filamin 1 / Endothelial actin-binding protein / Actin-binding protein 280 / ABP-280 / Nonmuscle filamin


Mass: 10075.146 Da / Num. of mol.: 1 / Fragment: Filamin A domain 17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P21333

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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
NMR detailsText: The numbering of residues in constraint and chemical shift files corresponds to the numbering of NMR construct (Residues 1-98).

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Sample preparation

DetailsContents: GAMV(1863-1956FLNA), U-13C, U-15N, NMR sample 0.3mM; 50mM sodium phosphate, 10mM dithiothreitol; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50mM / pH: 6.7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian Unity INOVA / Manufacturer: Varian / Model: Unity INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inc.processing
Sparky3.106T.D.Goddard, D.G.Knellerdata analysis
CYANA2P.G.ntert, C.Mumenthaler, K.W.thrichstructure solution
Amber8refinement
RefinementMethod: The structure calculations were made with the program CYANA 2.0 using the automated NOE assignment, structure calculation algorithm. The structure refinement of the 20 final CYANA structures ...Method: The structure calculations were made with the program CYANA 2.0 using the automated NOE assignment, structure calculation algorithm. The structure refinement of the 20 final CYANA structures was made with AMBER 8.0 program using the generalized Born continuum solvent model.
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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