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- PDB-3hor: Structure of the actin-binding domain of human filamin A (reduced) -

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Basic information

Entry
Database: PDB / ID: 3hor
TitleStructure of the actin-binding domain of human filamin A (reduced)
ComponentsFilamin-A
KeywordsSTRUCTURAL PROTEIN / Calponin homology domain / actin binding domain / Acetylation / Actin-binding / Alternative splicing / 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 / 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 / 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 / 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 / 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 / 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
Filamin family / Calponin-like domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Actin-binding Protein, T-fimbrin; domain 1 / 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. ...Filamin family / Calponin-like domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Actin-binding Protein, T-fimbrin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Filamin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsClark, A.R. / Sawyer, G.M. / Robertson, S.P. / Sutherland-Smith, A.J.
CitationJournal: Hum.Mol.Genet. / Year: 2009
Title: Skeletal dysplasias due to filamin A mutations result from a gain-of-function mechanism distinct from allelic neurological disorders
Authors: Clark, A.R. / Sawyer, G.M. / Robertson, S.P. / Sutherland-Smith, A.J.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)61,3856
Polymers61,0052
Non-polymers3804
Water54030
1
A: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6933
Polymers30,5031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6933
Polymers30,5031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.672, 72.290, 155.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELYSLYSchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA44 - 5847 - 61
12ARGARGTHRTHRchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA63 - 9866 - 101
13ARGARGPROPROchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA100 - 153103 - 156
14LEULEUPHEPHEchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA172 - 264175 - 267
21ILEILELYSLYSchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB44 - 5847 - 61
22ARGARGTHRTHRchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB63 - 9866 - 101
23ARGARGPROPROchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB100 - 153103 - 156
24LEULEUPHEPHEchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB172 - 264175 - 267

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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: 30502.670 Da / Num. of mol.: 2 / Fragment: Actin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNA / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21333
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 0.2M lithium sulfate, 0.1M Tris HCl, 5mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2007 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→42.1 Å / Num. obs: 17832 / % possible obs: 96.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.98 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 / Num. measured all: 72824
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / Num. unique all: 2487 / % possible all: 84

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HOP

3hop


Resolution: 2.7→42.092 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.98 / σ(F): 1.24 / Phase error: 29.3 / Stereochemistry target values: MLHL
Details: THE REFINEMENT PROGRAM REFMAC 5.5.0072 WAS ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 1561 5 %RANDOM; same as starting model
Rwork0.2251 29688 --
obs0.2284 16914 90.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.539 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 199.49 Å2 / Biso mean: 46.999 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1--4.075 Å20 Å2-0 Å2
2--16.98 Å20 Å2
3----12.905 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 20 30 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083461
X-RAY DIFFRACTIONf_angle_d1.0974702
X-RAY DIFFRACTIONf_chiral_restr0.072532
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d16.8131288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1587X-RAY DIFFRACTIONPOSITIONAL0.496
12B1587X-RAY DIFFRACTIONPOSITIONAL0.496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78720.39761550.31822487X-RAY DIFFRACTION84
2.7872-2.88680.44481430.30172537X-RAY DIFFRACTION85
2.8868-3.00230.38961110.2842653X-RAY DIFFRACTION89
3.0023-3.13890.29211120.26162670X-RAY DIFFRACTION89
3.1389-3.30430.29321480.24392719X-RAY DIFFRACTION91
3.3043-3.51130.2761320.22212755X-RAY DIFFRACTION93
3.5113-3.78220.29271560.2052795X-RAY DIFFRACTION93
3.7822-4.16250.25271680.17452758X-RAY DIFFRACTION94
4.1625-4.76420.23551550.17242789X-RAY DIFFRACTION93
4.7642-5.99960.27461360.19292754X-RAY DIFFRACTION93
5.9996-42.09750.25261450.20972771X-RAY DIFFRACTION93
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)
10.9499-0.1576-0.38510.34050.1110.5267-0.0501-0.43510.13440.02050.0131-0.1020.09750.12720.03580.05710.0979-0.0355-0.0308-0.05420.0688-19.9719-5.043527.1185
20.8528-0.0078-0.52670.5066-1.11093.2424-0.10610.1236-0.0309-0.3194-0.0186-0.02750.6595-0.42850.08370.1426-0.00250.0170.080.03520.0633-12.9509-26.746313.6132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA43 - 264
2X-RAY DIFFRACTION2chain BB44 - 269

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