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- PDB-9lxg: Filamin A repeat 21 in complex with LARP4 Ala269-Asn281 peptide -

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Basic information

Entry
Database: PDB / ID: 9lxg
TitleFilamin A repeat 21 in complex with LARP4 Ala269-Asn281 peptide
Components
  • Filamin-A
  • La-related protein 4
KeywordsPROTEIN BINDING / FLNA / LARP4 / mechanosensing
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 / 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 / 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 / blood coagulation, intrinsic pathway / tubulin deacetylation / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / protein localization to bicellular tight junction / Fc-gamma receptor I complex binding / Cell-extracellular matrix interactions / apical dendrite / positive regulation of potassium ion transmembrane transport / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / regulation of cell morphogenesis / 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 / SMAD binding / receptor clustering / cortical cytoskeleton / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / cilium assembly / mitotic spindle assembly / potassium channel regulator activity / negative regulation of DNA-binding transcription factor activity / release of sequestered calcium ion into cytosol / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / protein sequestering activity / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / actin filament / establishment of protein localization / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / cerebral cortex development / negative regulation of protein catabolic process / positive regulation of protein import into nucleus / small GTPase binding / platelet aggregation / kinase binding / Z disc / cytoplasmic stress granule / actin filament binding / cell-cell junction / Platelet degranulation / actin cytoskeleton / growth cone / GTPase binding / actin cytoskeleton organization / perikaryon / DNA-binding transcription factor binding / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / postsynapse / protein stabilization / cadherin binding / translation / 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 / cytoplasm / cytosol
Similarity search - Function
LARP4, RNA recognition motif / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat ...LARP4, RNA recognition motif / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / 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. / RNA-binding domain superfamily / Immunoglobulin E-set / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Filamin-A / La-related protein 4
Similarity search - Component
Biological speciesEsselenichthys carli (threeline prickleback)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsMao, Z.F. / Yuanyuan, D.
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 18, 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
A: Filamin-A
B: La-related protein 4


Theoretical massNumber of molelcules
Total (without water)11,6762
Polymers11,6762
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-8 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.040, 78.040, 32.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,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: 10179.178 Da / Num. of mol.: 1
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: Protein/peptide La-related protein 4 / La ribonucleoprotein domain family member 4


Mass: 1496.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Esselenichthys carli (threeline prickleback)
Gene: Larp4
Production host: Esselenichthys carli (threeline prickleback)
References: UniProt: Q8BWW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Lithium sulfate, 0.1 M Sodium citrate pH 5.6, 0.5 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→24.91 Å / Num. obs: 4156 / % possible obs: 99.54 % / Redundancy: 17.5 % / Biso Wilson estimate: 33.36 Å2 / CC1/2: 0.997 / Net I/σ(I): 21.47
Reflection shellResolution: 2.46→2.54 Å / Mean I/σ(I) obs: 13 / Num. unique obs: 405 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→24.91 Å / SU ML: 0.2085 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 17.165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2593 204 4.91 %
Rwork0.204 3947 -
obs0.2069 4151 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.53 Å2
Refinement stepCycle: LAST / Resolution: 2.46→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 11 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093819
X-RAY DIFFRACTIONf_angle_d1.01361107
X-RAY DIFFRACTIONf_chiral_restr0.056116
X-RAY DIFFRACTIONf_plane_restr0.0115150
X-RAY DIFFRACTIONf_dihedral_angle_d16.7716295
LS refinement shellResolution: 2.46→24.91 Å
RfactorNum. reflection% reflection
Rfree0.2593 204 -
Rwork0.204 3947 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: -10.3969627697 Å / Origin y: 23.2802673756 Å / Origin z: 4.81525846033 Å
111213212223313233
T0.195134325488 Å20.00483314681917 Å20.0228836951784 Å2-0.171367473338 Å20.0242494922138 Å2--0.214711172816 Å2
L2.61024920473 °20.650076945385 °20.330368808646 °2-2.28554807573 °2-0.941707509758 °2--2.22021669577 °2
S-0.0433566712262 Å °-0.0709882265798 Å °-0.311668117558 Å °-0.0768145033958 Å °0.123937580394 Å °0.0176310934999 Å °0.220495642111 Å °-0.110083451717 Å °-0.105322571511 Å °
Refinement TLS groupSelection details: all

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