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- PDB-7sc4: filamin complex-1 -

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Basic information

Entry
Database: PDB / ID: 7sc4
Titlefilamin complex-1
ComponentsFilamin-A/Integrin alpha-IIb light chain, form 2 chimera
KeywordsCELL ADHESION / filamin / integrin / inside-out signaling / outside-in signaling
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 / formation of radial glial scaffolds / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / 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 / formation of radial glial scaffolds / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / OAS antiviral response / positive regulation of actin filament bundle assembly / platelet alpha granule membrane / positive regulation of neuron migration / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / fibrinogen binding / early endosome to late endosome transport / apical dendrite / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / extracellular matrix binding / protein localization to cell surface / integrin complex / positive regulation of leukocyte migration / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / Fc-gamma receptor I complex binding / cell adhesion mediated by integrin / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / p130Cas linkage to MAPK signaling for integrins / receptor clustering / positive regulation of axon regeneration / actin filament bundle / SMAD binding / RHO GTPases activate PAKs / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / semaphorin-plexin signaling pathway / cilium assembly / mitotic spindle assembly / ECM proteoglycans / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / Integrin cell surface interactions / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / regulation of cell migration / Integrin signaling / cell-matrix adhesion / protein kinase C binding / dendritic shaft / Signal transduction by L1 / G protein-coupled receptor binding / actin filament / integrin-mediated signaling pathway / protein localization to plasma membrane / synapse organization / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mRNA transcription by RNA polymerase II / MAP2K and MAPK activation / establishment of protein localization / trans-Golgi network / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / cell-cell adhesion / cerebral cortex development / platelet aggregation / small GTPase binding / Z disc / kinase binding / 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 / cell-cell junction / actin cytoskeleton / integrin binding / negative regulation of neuron projection development / Platelet degranulation / GTPase binding / perikaryon / actin cytoskeleton organization / postsynapse / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / blood microparticle
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Actinin-type actin-binding domain signature 1. ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Integrin alpha-IIb / Filamin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
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
DepositionSep 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamin-A/Integrin alpha-IIb light chain, form 2 chimera
B: Filamin-A/Integrin alpha-IIb light chain, form 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7633
Polymers26,6672
Non-polymers961
Water1,982110
1
A: Filamin-A/Integrin alpha-IIb light chain, form 2 chimera


Theoretical massNumber of molelcules
Total (without water)13,3331
Polymers13,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Filamin-A/Integrin alpha-IIb light chain, form 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4292
Polymers13,3331
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.248, 66.010, 71.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Filamin-A/Integrin alpha-IIb light chain, form 2 chimera / 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: 13333.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNA, FLN, FLN1, ITGA2B, GP2B, ITGAB / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P21333, UniProt: P08514
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 2 M Ammonium Sulfate, 5% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 55864 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Χ2: 1.36 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3 / Num. unique obs: 604 / Χ2: 1.12 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.27data extraction
HKL-3000v1.0data reduction
HKL-3000v1.0data scaling
PHASERv1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BRQ

2brq


Resolution: 1.85→35.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.114 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1082 5.1 %RANDOM
Rwork0.1987 ---
obs0.2019 19972 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.89 Å2 / Biso mean: 34.845 Å2 / Biso min: 16.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.85→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 5 110 1714
Biso mean--64.59 40.17 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191722
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9492346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4995235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97123.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94815248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1021511
X-RAY DIFFRACTIONr_chiral_restr0.1450.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0221379
LS refinement shellResolution: 1.85→1.896 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 93 -
Rwork0.263 1409 -
obs--98.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54120.1912-0.28761.0233-0.30950.9022-0.02030.01130.0051-0.04710.0544-0.00980.04740.1375-0.03410.08280.00730.02760.037-0.00660.012211.844-19.28-13.499
20.4046-0.41160.27982.2509-1.17810.71980.06280.08490.01140.1908-0.2384-0.1687-0.13010.14310.17550.0748-0.0148-0.06870.03210.02480.100914.111-13.66610.999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2236 - 2329
2X-RAY DIFFRACTION2B2236 - 2329

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