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- PDB-3rgh: Structure of filamin A immunoglobulin-like repeat 10 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 3rgh
TitleStructure of filamin A immunoglobulin-like repeat 10 from Homo sapiens
ComponentsFilamin-A
KeywordsCELL ADHESION / CYTOSKELETON-COMPLEX / DISEASE MUTATION / IMMUNOGLOBULIN LIKE / FILAMIN / CYTOSKELETON / ACTIN-BINDING / CELL JUNCTION / CELL SHAPE / Immunoglobulin-like beta-sandwich / CD4 / beta-mercaptoethanol adduct
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 / 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 / actin crosslink formation / tubulin deacetylation / 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 / Cell-extracellular matrix interactions / early endosome to late endosome transport / Fc-gamma receptor I complex binding / positive regulation of potassium ion transmembrane transport / apical dendrite / 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 / podosome / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / receptor clustering / positive regulation of axon regeneration / cortical cytoskeleton / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / brush border / semaphorin-plexin signaling pathway / cilium assembly / blood vessel remodeling / mitotic spindle assembly / epithelial to mesenchymal transition / potassium channel regulator activity / axonal growth cone / heart morphogenesis / 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 kinase C binding / protein localization to plasma membrane / actin filament / negative regulation of DNA-binding transcription factor activity / trans-Golgi network / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / establishment of protein localization / synapse organization / negative regulation of protein catabolic process / cerebral cortex development / small GTPase binding / Z disc / kinase binding / platelet aggregation / positive regulation of protein import into nucleus / actin filament binding / cell-cell junction / Platelet degranulation / actin cytoskeleton / negative regulation of neuron projection development / actin cytoskeleton organization / GTPase binding / angiogenesis / 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 / nucleus / membrane / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Filamin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsPage, R.C. / Clark, J. / Misra, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of filamin A immunoglobulin-like repeat 10 from Homo sapiens.
Authors: Page, R.C. / Clark, J.G. / Misra, S.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Apr 3, 2024Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)21,0014
Polymers20,8832
Non-polymers1182
Water1,38777
1
A: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5012
Polymers10,4421
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5012
Polymers10,4421
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.453, 50.549, 107.172
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-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 156:197 OR RESSEQ 199:252 )
211CHAIN B AND (RESSEQ 156:197 OR RESSEQ 199:252 )
DetailsAuthors state that the biological unit is a monomer. The disulfide bond between monomers is a crystallographic artifact.

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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: 10441.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLN, FLN1, FLNA / Plasmid: pGST parallel-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P21333
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium acetate, 25%(w/v) PEG 3350, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 18, 2010 / Details: mirrors
RadiationMonochromator: VariMax confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→34.51 Å / Num. all: 7677 / Num. obs: 7677 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.55 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 4.43 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 5.5 / Num. unique all: 755 / % possible all: 90.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX1.7_650model building
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: iTASSER homology model

Resolution: 2.44→30.14 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.16 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 758 10 %RANDOM
Rwork0.2289 ---
all0.234 7577 --
obs0.2339 7577 97.13 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.323 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.2293 Å20 Å2-0 Å2
2---5.1273 Å20 Å2
3---1.898 Å2
Refinement stepCycle: LAST / Resolution: 2.44→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 8 77 1519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011475
X-RAY DIFFRACTIONf_angle_d1.1772008
X-RAY DIFFRACTIONf_dihedral_angle_d14.101534
X-RAY DIFFRACTIONf_chiral_restr0.073223
X-RAY DIFFRACTIONf_plane_restr0.009271
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A703X-RAY DIFFRACTIONPOSITIONAL
12B703X-RAY DIFFRACTIONPOSITIONAL0.46
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.44-2.63080.43241400.36161268140893
2.6308-2.89530.44891470.30621320146797
2.8953-3.31380.29891510.23551362151398
3.3138-4.17330.25631550.21041390154599
4.1733-30.14240.21791650.19591479164499
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)
10.03250.0021-0.01670.02020.02750.0472-0.00830.0555-0.035-0.00410.033-0.00780.1016-0.03750.00590.30730.04480.1050.10460.11970.04645.175918.84-26.4572
20.3393-0.2168-0.13220.63690.34790.2079-0.1266-0.129-0.1772-0.2541-0.0184-0.2193-0.10230.07220.01670.2470.07810.07740.2070.06450.36541.59350.842-10.0125
30.16940.2974-0.21071.1589-0.92150.9789-0.22060.10810.0014-0.28170.0404-0.28-0.1145-0.21860.10930.22850.00410.02010.15650.00980.1592-1.108212.6952-16.7339
40.1710.1105-0.03640.0718-0.05580.1475-0.0313-0.0304-0.034-0.0542-0.0224-0.0568-0.0009-0.01080.0010.2901-0.13020.08590.2457-0.06890.3565-13.25311.9665-12.4617
50.05410.0516-0.04270.0493-0.02940.1381-0.23240.12560.037-0.0019-0.15210.0127-0.0016-0.0207-0.0089-0.5736-0.46340.0596-0.09950.03710.1894-0.328613.9548-9.9812
60.4636-0.006-0.23360.2834-0.55781.2969-0.09080.0044-0.26430.05150.08980.16480.1827-0.00030.04560.1651-0.00830.04170.1057-0.01090.219-6.73164.7148-16.9258
70.0019-0.00160.01190.0008-0.00650.06680.07060.12410.1222-0.0066-0.00990.04980.0187-0.09260.01730.2846-0.11850.1080.2283-0.08490.1524-0.92387.3534-25.0331
80.05390.0223-0.02350.2108-0.04470.1201-0.01570.0340.03270.1439-0.0545-0.06820.0803-0.0269-0.01220.2571-0.02310.08250.1098-0.01150.1635-3.8688-5.4743-10.6217
90.1693-0.0731-0.06610.03090.01950.02670.0496-0.003-0.1382-0.03140.09730.054-0.0091-0.0751-0.03290.63840.0206-0.04640.50890.14530.5138-13.875130.0162-23.2406
100.0188-0.0209-0.02260.0230.04140.1894-0.0258-0.0916-0.0797-0.018-0.01630.0902-0.0581-0.17650.00390.14670.06670.01980.2397-0.0440.2758-14.641929.0033-6.8254
110.148-0.09120.00150.2761-0.020.00510.1290.17580.0581-0.1741-0.08320.03180.0018-0.1456-0.0220.1670.01830.0040.27090.05270.1258-11.972425.4001-3.9382
120.29890.26330.50710.53670.70381.0385-0.1842-0.00270.0476-0.11530.0039-0.16950.1564-0.20650.06690.2724-0.0499-0.02150.19620.0120.1324-2.543526.934-11.8595
130.2202-0.0938-0.15860.2126-0.09020.2427-0.08090.0180.1098-0.0189-0.0259-0.12040.0437-0.0820.02520.1618-0.0648-0.04590.23060.0080.1897-0.943323.945-3.649
140.5543-0.2903-0.17770.8326-0.22740.90390.00420.22090.2062-0.0095-0.0009-0.2431-0.0065-0.0617-0.0020.17290.0258-0.04270.23680.02240.2386-6.541525.5431-4.5382
150.30050.0072-0.13730.24050.07130.0889-0.1851-0.0916-0.0943-0.0904-0.04580.0799-0.2291-0.13450.11330.26190.0490.02470.13550.01730.2978-7.376232.1013-17.6798
160.30440.12110.04460.0683-0.01240.237-0.21240.04360.245-0.04770.13450.15790.0692-0.0080.03590.34310.0759-0.01860.10860.00130.2603-6.76933.96841.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 155:164)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 165:177)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 178:198)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 199:206)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 207:223)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 224:237)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 238:245)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 246:252)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 155:162)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 163:170)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 171:189)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 190:198)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 199:211)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 212:234)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 235:241)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 242:252)

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