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- PDB-7sft: Filamin complex-2 -

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Basic information

Entry
Database: PDB / ID: 7sft
TitleFilamin complex-2
Components
  • Filamin-A
  • Integrin alpha-IIb light chain, form 2
KeywordsSIGNALING PROTEIN / filamin / integrin / inside-out signaling / outside-in signaling / cell adhesion
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 / integrin alphaIIb-beta3 complex / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / platelet alpha granule membrane / Cell-extracellular matrix interactions / early endosome to late endosome transport / fibrinogen binding / 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 / extracellular matrix binding / positive regulation of leukocyte migration / integrin complex / wound healing, spreading of cells / podosome / negative regulation of transcription by RNA polymerase I / megakaryocyte development / cell adhesion mediated by integrin / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / receptor clustering / positive regulation of axon regeneration / cortical cytoskeleton / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / GRB2:SOS provides linkage to MAPK signaling for Integrins / brush border / semaphorin-plexin signaling pathway / cilium assembly / blood vessel remodeling / mitotic spindle assembly / epithelial to mesenchymal transition / ECM proteoglycans / Integrin cell surface interactions / potassium channel regulator activity / axonal growth cone / heart morphogenesis / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / Integrin signaling / protein sequestering activity / regulation of cell migration / dendritic shaft / protein kinase C binding / cell-matrix adhesion / protein localization to plasma membrane / Signal transduction by L1 / integrin-mediated signaling pathway / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / negative regulation of protein catabolic process / cerebral cortex development / cell-cell adhesion / small GTPase binding / Z disc / kinase binding / platelet aggregation / positive regulation of protein import into nucleus / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / Signaling by BRAF and RAF1 fusions / integrin 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 / molecular adaptor activity
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 / : ...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 / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Calponin homology domain / Integrin domain superfamily / Integrin alpha, N-terminal / 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
Integrin alpha-IIb / Filamin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, J. / Qin, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL58758 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL73311 United States
American Heart Association18CDA34110364 United States
CitationJournal: Blood / Year: 2023
Title: A mechanism of platelet integrin alpha IIb beta 3 outside-in signaling through a novel integrin alpha IIb subunit-filamin-actin linkage.
Authors: Liu, J. / Lu, F. / Ithychanda, S.S. / Apostol, M. / Das, M. / Deshpande, G. / Plow, E.F. / Qin, J.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamin-A
B: Integrin alpha-IIb light chain, form 2


Theoretical massNumber of molelcules
Total (without water)12,3452
Polymers12,3452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1480 Å2
ΔGint-7 kcal/mol
Surface area7820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9762.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNA, FLN, FLN1 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P21333
#2: Protein/peptide Integrin alpha-IIb light chain, form 2


Mass: 2581.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Production host: Escherichia coli (E. coli) / References: UniProt: P08514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-1H NOESY
123isotropic12D 1H-1H TOCSY
131isotropic23D HN(CO)CA
141isotropic23D CBCA(CO)NH
151isotropic23D (H)CCH-TOCSY
161isotropic23D HN(CA)CB
171isotropic23D 1H-15N NOESY
182isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] filamin Ig21, 2 mM Integrin alpha-IIb light chain, 90% H2O/10% D2Oin 50mM 20% PIP2 inserted PSPC vesicle buffer solution15N-13C90% H2O/10% D2O
solution21 mM [U-15N; U-2H] filamin Ig21, 2 mM Integrin alpha-IIb light chain, 90% H2O/10% D2Oin 50mM 20% PIP2 inserted PSPC vesicle buffer solution2D-15N90% H2O/10% D2O
solution32 mM Integrin alpha-IIb light chain, 0.05 mM GST-filamin-Ig21, 90% H2O/10% D2Oin 50mM 20% PIP2 inserted PSPC vesicle buffer solutiontr-NOE90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMfilamin Ig21[U-100% 13C; U-100% 15N]1
2 mMIntegrin alpha-IIb light chainnatural abundance1
1 mMfilamin Ig21[U-15N; U-2H]2
2 mMIntegrin alpha-IIb light chainnatural abundance2
2 mMIntegrin alpha-IIb light chainnatural abundance3
0.05 mMGST-filamin-Ig21natural abundance3
Sample conditionsDetails: 25mM Sodium Phosphate PH 6.4, 5mM NaCl, 1mM TCEP / Ionic strength: 61 mM / Label: conditions_1 / pH: 6.4 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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