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- PDB-4p3w: Crystal structure of the human filamin A Ig-like domains 20-21 in... -

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Basic information

Entry
Database: PDB / ID: 4p3w
TitleCrystal structure of the human filamin A Ig-like domains 20-21 in complex with migfilin peptide
Components
  • Filamin-A
  • Filamin-binding LIM protein 1
KeywordsCELL ADHESION / cytoskeleton / adhesion / immunoglobulin-like / actin binding protein
Function / homology
Function and homology information


regulation of integrin activation / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / filamin binding / 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 ...regulation of integrin activation / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / filamin binding / 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 / stress fiber / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / protein sequestering activity / regulation of cell migration / dendritic shaft / cell periphery / protein localization to plasma membrane / actin filament / establishment of protein localization / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / cell-cell adhesion / cerebral cortex development / negative regulation of protein catabolic process / positive regulation of protein import into nucleus / small GTPase binding / platelet aggregation / kinase binding / fibrillar center / Z disc / actin filament binding / cell-cell junction / cell junction / Platelet degranulation / regulation of cell shape / 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 / metal ion binding / nucleus / membrane / 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 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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
PRASEODYMIUM ION / Filamin-A / Filamin-binding LIM protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeppala, J. / Pentikainen, U. / Ylanne, J.
CitationJournal: To Be Published
Title: Crystal structure of the human filamin A Ig-like domains 20-21 in complex with migfilin peptide
Authors: Seppala, J. / Pentikainen, U. / Ylanne, J.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Structure summary
Category: pdbx_struct_oper_list / software / struct_keywords
Item: _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 23, 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
G: Filamin-binding LIM protein 1
H: Filamin-binding LIM protein 1
E: Filamin-A
F: Filamin-A
K: Filamin-binding LIM protein 1
L: Filamin-binding LIM protein 1
D: Filamin-A
C: Filamin-A
J: Filamin-binding LIM protein 1
I: Filamin-binding LIM protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,81122
Polymers129,81712
Non-polymers99410
Water2,108117
1
A: Filamin-A
G: Filamin-binding LIM protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8734
Polymers21,6362
Non-polymers2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Filamin-A
H: Filamin-binding LIM protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8734
Polymers21,6362
Non-polymers2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Filamin-A
K: Filamin-binding LIM protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8965
Polymers21,6362
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Filamin-A
L: Filamin-binding LIM protein 1


Theoretical massNumber of molelcules
Total (without water)21,6362
Polymers21,6362
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Filamin-A
J: Filamin-binding LIM protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7773
Polymers21,6362
Non-polymers1411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: Filamin-A
I: Filamin-binding LIM protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7554
Polymers21,6362
Non-polymers1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.154, 88.154, 394.709
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11E-2402-

NA

21C-2402-

NA

31E-2516-

HOH

41C-2502-

HOH

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABEFDCGHKLJI

#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: 19023.158 Da / Num. of mol.: 6 / Fragment: Filamin repeats 20 and 21, residues 2152-2329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNA, FLN, FLN1 / Plasmid: pGEX4T3-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P21333
#2: Protein/peptide
Filamin-binding LIM protein 1 / FBLP-1 / Migfilin / Mitogen-inducible 2-interacting protein / MIG2-interacting protein


Mass: 2613.020 Da / Num. of mol.: 6 / Fragment: residues 5-28 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WUP2

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Non-polymers , 4 types, 127 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pr
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M MES pH 6, 1.9 M (NH4)2SO4, 0.1 M (CH3CO2)3Pr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2012
RadiationMonochromator: Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.8→45.36 Å / Num. obs: 103427 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.426 % / Biso Wilson estimate: 40.614 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.062 / Rsym value: 0.062 / Χ2: 0.985 / Net I/σ(I): 14.07 / Num. measured all: 354375
Reflection shell
Diffraction-IDRejects
10
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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHASERphasing
PDB_EXTRACT3.14data extraction
XDSdata reduction
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BRQ

2brq


Resolution: 2→43.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2103 / WRfactor Rwork: 0.1939 / FOM work R set: 0.8367 / SU B: 5.86 / SU ML: 0.088 / SU R Cruickshank DPI: 0.0386 / SU Rfree: 0.0324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 3863 5 %RANDOM
Rwork0.2003 ---
obs0.2016 73110 99.57 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.75 Å2 / Biso mean: 25.435 Å2 / Biso min: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1--7.92 Å2-0 Å2-0 Å2
2---7.92 Å2-0 Å2
3---15.84 Å2
Refinement stepCycle: final / Resolution: 2→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7957 0 26 117 8100
Biso mean--55.62 37.06 -
Num. residues----1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198170
X-RAY DIFFRACTIONr_bond_other_d0.0110.027580
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.95211096
X-RAY DIFFRACTIONr_angle_other_deg1.946317588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05451070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24124.363314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.157151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9271532
X-RAY DIFFRACTIONr_chiral_restr0.1220.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0219212
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021690
X-RAY DIFFRACTIONr_mcbond_it1.8152.424340
X-RAY DIFFRACTIONr_mcbond_other1.8132.424339
X-RAY DIFFRACTIONr_mcangle_it2.7053.6145390
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 301 -
Rwork0.284 5438 -
all-5739 -
obs--99.74 %
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)
11.5762-0.587-0.41331.05310.91312.0895-0.0296-0.0067-0.0830.0152-0.04820.10260.0479-0.20320.07780.0224-0.0235-0.02290.04020.01140.251521.7526.916109.328
20.68830.06370.44181.8804-0.74372.2965-0.0470.0330.0325-0.0205-0.0265-0.1308-0.15780.13780.07350.0161-0.01650.0010.0296-0.02620.259727.1210.025111.619
31.0175-0.3882-0.54551.80291.58152.35470.0159-0-0.08380.00920.026-0.08470.03350.0776-0.04180.0960.0119-0.04070.1080.00790.325626.082-10.18765.573
42.13010.72080.76391.93961.04982.7225-0.050.1520.0712-0.30390.00570.0584-0.29940.18540.04430.15120.0689-0.0130.1318-0.02260.312822.681-7.53860.562
50.96130.74150.87271.63011.54032.56850.00470.02360.0633-0.0413-0.0017-0.016-0.02140.0508-0.0030.0325-0.00440.02610.0567-0.0030.297426.0610.14823.654
62.1555-0.5801-0.93912.29141.60123.1394-0.0266-0.1176-0.06080.3351-0.05360.08250.37860.0470.08020.1032-0.06790.0180.1065-0.02740.255121.8738.34729.327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2158 - 2329
2X-RAY DIFFRACTION1H6 - 20
3X-RAY DIFFRACTION2B2159 - 2329
4X-RAY DIFFRACTION2G6 - 20
5X-RAY DIFFRACTION3C2157 - 2328
6X-RAY DIFFRACTION3J7 - 19
7X-RAY DIFFRACTION4D2158 - 2328
8X-RAY DIFFRACTION4I7 - 20
9X-RAY DIFFRACTION5E2157 - 2328
10X-RAY DIFFRACTION5L7 - 18
11X-RAY DIFFRACTION6F2159 - 2328
12X-RAY DIFFRACTION6K6 - 20

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