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- PDB-9lwx: Crystal structure of the Filamin A repeat 21 -

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Basic information

Entry
Database: PDB / ID: 9lwx
TitleCrystal structure of the Filamin A repeat 21
ComponentsFilamin-A
KeywordsSIGNALING PROTEIN / Filamin / mechanotransduction
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 / formation of radial glial scaffolds / Myb complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / protein localization to bicellular tight junction / positive regulation of integrin-mediated signaling pathway / positive regulation of neuron migration / blood coagulation, intrinsic pathway ...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 / formation of radial glial scaffolds / Myb complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / protein localization to bicellular tight junction / positive regulation of integrin-mediated signaling pathway / positive regulation of neuron migration / blood coagulation, intrinsic pathway / OAS antiviral response / actin crosslink formation / positive regulation of actin filament bundle assembly / tubulin deacetylation / megakaryocyte development / Cell-extracellular matrix interactions / positive regulation of platelet activation / positive regulation of potassium ion transmembrane transport / protein localization to cell surface / apical dendrite / positive regulation of neural precursor cell proliferation / Fc-gamma receptor I complex binding / podosome / negative regulation of transcription by RNA polymerase I / wound healing, spreading of cells / GP1b-IX-V activation signalling / receptor clustering / SMAD binding / cortical cytoskeleton / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / mitotic spindle assembly / potassium channel regulator activity / positive regulation of substrate adhesion-dependent cell spreading / cilium assembly / release of sequestered calcium ion into cytosol / regulation of cell migration / protein localization to plasma membrane / dendritic shaft / actin filament / establishment of protein localization / negative regulation of protein catabolic process / positive regulation of protein import into nucleus / cerebral cortex development / protein sequestering activity / platelet aggregation / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / kinase binding / small GTPase binding / Z disc / cell-cell junction / actin filament binding / actin cytoskeleton organization / actin cytoskeleton / Platelet degranulation / growth cone / GTPase binding / 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 / membrane / nucleus / 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
Similarity search - Domain/homology
Biological speciesEsselenichthys carli (threeline prickleback)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsMao, Z.F. / Yirong, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070777 China
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Structural Basis of the LARP4-Filamin A Interaction and Competition with Integrin beta 7 Tails.
Authors: Mao, Z. / Ding, Y. / Liu, Y. / Mei, K. / Nakamura, F.
History
DepositionFeb 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

Downloads & links

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Assembly

Deposited unit
D: Filamin-A
A: Filamin-A
B: Filamin-A
C: Filamin-A


Theoretical massNumber of molelcules
Total (without water)40,2084
Polymers40,2084
Non-polymers00
Water1,29772
1
D: Filamin-A


Theoretical massNumber of molelcules
Total (without water)10,0521
Polymers10,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Filamin-A


Theoretical massNumber of molelcules
Total (without water)10,0521
Polymers10,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Filamin-A


Theoretical massNumber of molelcules
Total (without water)10,0521
Polymers10,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Filamin-A


Theoretical massNumber of molelcules
Total (without water)10,0521
Polymers10,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.694, 47.912, 50.360
Angle α, β, γ (deg.)78.421, 83.693, 90.096
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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: 10052.071 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Esselenichthys carli (threeline prickleback)
Gene: FLNA, FLN, FLN1
Production host: Esselenichthys carli (threeline prickleback)
References: UniProt: P21333
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate, pH 6.5, 30% w/ Polyethylene glycol (PEG) 8,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→28.27 Å / Num. obs: 13931 / % possible obs: 90.1 % / Redundancy: 13 % / Biso Wilson estimate: 38.28 Å2 / CC1/2: 0.93 / Net I/σ(I): 8
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 883 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→28.27 Å / SU ML: 0.3068 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.9475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 653 4.69 %
Rwork0.2201 13278 -
obs0.2224 13931 90.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.32 Å2
Refinement stepCycle: LAST / Resolution: 2.29→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 0 72 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472844
X-RAY DIFFRACTIONf_angle_d0.82043859
X-RAY DIFFRACTIONf_chiral_restr0.0633400
X-RAY DIFFRACTIONf_plane_restr0.006531
X-RAY DIFFRACTIONf_dihedral_angle_d17.79881023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.460.3189820.28121921X-RAY DIFFRACTION65.18
2.46-2.710.36851350.30092771X-RAY DIFFRACTION93.47
2.71-3.10.32311430.272847X-RAY DIFFRACTION96.86
3.1-3.910.29411410.21822888X-RAY DIFFRACTION97.68
3.91-28.270.20191520.17432851X-RAY DIFFRACTION97.15

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