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- PDB-3cnk: Crystal Structure of the dimerization domain of human filamin A -

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Basic information

Entry
Database: PDB / ID: 3cnk
TitleCrystal Structure of the dimerization domain of human filamin A
ComponentsFilamin-A
KeywordsSTRUCTURAL PROTEIN / Filamin / FLNa24 / X-ray crystalography / homodimer / Acetylation / Actin-binding / Cytoplasm / Cytoskeleton / Disease mutation / Phosphoprotein / Polymorphism
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 / 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 / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / 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 / positive regulation of neuron migration / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / early endosome to late endosome transport / apical dendrite / Fc-gamma receptor I complex binding / 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 / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / positive regulation of axon regeneration / receptor clustering / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / brush border / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / small GTPase binding / kinase binding / platelet aggregation / Z disc / positive regulation of protein import into nucleus / cell-cell junction / actin filament binding / actin cytoskeleton / Platelet degranulation / GTPase binding / negative regulation of neuron projection development / actin cytoskeleton organization / postsynapse / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / protein stabilization / cadherin binding / focal adhesion / glutamatergic synapse / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLee, B.J. / Seo, M.D. / Seok, S.H. / Lee, S.J. / Kwon, A.R. / Im, H.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the dimerization domain of human filamin A
Authors: Seo, M.-D. / Seok, S.-H. / Im, H. / Kwon, A.-R. / Lee, S.-J. / Kim, H.-R. / Cho, Y. / Park, D. / Lee, B.-J.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Filamin-A
B: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5854
Polymers19,3932
Non-polymers1922
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-35 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.845, 94.642, 40.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / Non-muscle filamin


Mass: 9696.328 Da / Num. of mol.: 2 / Fragment: Filamin 24, repeat 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNA, FLN, FLN1 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21333
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS REFERRED IN REF 2 IN P21333.

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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: 2.89 Å3/Da / Density % sol: 57.47 % / Mosaicity: 0.98 °
Crystal growTemperature: 293 K / pH: 8.2
Details: 0.1M Tris, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 27127 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.054 / Χ2: 0.988 / Net I/av σ(I): 17.4 / Net I/σ(I): 31.708 / Num. measured all: 167922
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.715.70.33227030.59599.3
1.71-1.786.20.24727370.63999.8
1.78-1.866.20.18527200.799.5
1.86-1.966.10.14327020.77699.1
1.96-2.086.20.11126990.93497.7
2.08-2.246.20.0926550.98796.8
2.24-2.466.20.07526261.01994.6
2.46-2.826.40.06225841.22292.6
2.82-3.556.30.0427281.46496.4
3.55-506.40.02929731.43299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V05

1v05


Resolution: 1.65→33.44 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.212 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.865 / SU B: 3.482 / SU ML: 0.055 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21855 1355 5 %RANDOM
Rwork0.19208 25712 --
obs0.19347 27067 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.83 Å2 / Biso mean: 18.227 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 10 184 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221404
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9871902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.90422.60946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.746156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021016
X-RAY DIFFRACTIONr_nbd_refined0.2060.2588
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2133
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.214
X-RAY DIFFRACTIONr_mcbond_it1.1831.5904
X-RAY DIFFRACTIONr_mcangle_it1.86621424
X-RAY DIFFRACTIONr_scbond_it2.8193571
X-RAY DIFFRACTIONr_scangle_it4.0784.5478
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 90 -
Rwork0.213 1918 -
all-2008 -
obs--99.9 %
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)
10.70080.1860.31180.68340.45841.24320.01230.0205-0.05010.00410.0348-0.0550.0115-0.0066-0.0471-0.0271-0.00490.0066-0.0213-0.0068-0.01899.981814.137912.6884
20.6776-0.31080.19050.5268-0.19351.00830.02730.0377-0.0251-0.01340.01380.05180.00490.0284-0.041-0.02070.0056-0.0025-0.01220.0058-0.0273-6.747216.247310.0316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2559 - 2647
2X-RAY DIFFRACTION2B2559 - 2647

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