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- PDB-2w0p: Crystal structure of the filamin A repeat 21 complexed with the m... -

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Basic information

Entry
Database: PDB / ID: 2w0p
TitleCrystal structure of the filamin A repeat 21 complexed with the migfilin peptide
Components
  • FILAMIN-A
  • FILAMIN-BINDING LIM PROTEIN 1
KeywordsCELL ADHESION / ALTERNATIVE SPLICING / CYTOSKELETON-COMPLEX / PHOSPHOPROTEIN / DISEASE MUTATION / IMMUNOGLOBULIN LIKE / ZINC / FILAMIN / COMPLEX / INTEGRIN / MIGFILIN / RECEPTOR / POLYMORPHISM / CYTOSKELETON / ACTIN-BINDING / CELL JUNCTION / METAL-BINDING / CYTOPLASM / LIM DOMAIN / CELL SHAPE / ACETYLATION
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 / tubulin deacetylation / blood coagulation, intrinsic pathway / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / protein localization to bicellular tight junction / Cell-extracellular matrix interactions / Fc-gamma receptor I complex binding / positive regulation of potassium ion transmembrane transport / apical dendrite / 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 / cortical cytoskeleton / SMAD binding / 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 / mRNA transcription by RNA polymerase II / establishment of protein localization / G protein-coupled receptor binding / cell-cell adhesion / negative regulation of protein catabolic process / cerebral cortex development / small GTPase binding / positive regulation of protein import into nucleus / platelet aggregation / kinase binding / fibrillar center / Z disc / actin filament binding / cell-cell junction / cell junction / Platelet degranulation / actin cytoskeleton / regulation of cell shape / 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 / 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 / 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
Filamin-A / Filamin-binding LIM protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRuskamo, S. / Ylanne, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis of the Migfilin-Filamin Interaction and Competition with Integrin {Beta} Tails.
Authors: Lad, Y. / Jiang, P. / Ruskamo, S. / Harburger, D.S. / Ylanne, J. / Campbell, I.D. / Calderwood, D.A.
History
DepositionAug 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
C: FILAMIN-BINDING LIM PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2205
Polymers21,0283
Non-polymers1922
Water1,26170
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-7.7 kcal/mol
Surface area12370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)36.890, 68.480, 85.220
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 2237 - 2328 / Label seq-ID: 2 - 93

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 / NONMUSCLE FILAMIN


Mass: 9705.669 Da / Num. of mol.: 2 / Fragment: IG-21, RESIDUES 2236-2329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21333
#2: Protein/peptide FILAMIN-BINDING LIM PROTEIN 1 / MITOGEN-INDUCIBLE 2-INTERACTING PROTEIN / MIGFILIN


Mass: 1616.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-19 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8WUP2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.51 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growDetails: 1.7M (NH4)2SO4, 5% 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2008 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→32.48 Å / Num. obs: 17625 / % possible obs: 99.9 % / Redundancy: 2.54 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.35 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BRQ, CHAIN A

2brq


Resolution: 1.9→32.48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.046 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2262 TRP, A 2287 ASP, A 2289 LYS, B 2252 GLU, B 2265 GLU, B 2268 ALA, B 2289 LYS, B 2313 GLU, B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2262 TRP, A 2287 ASP, A 2289 LYS, B 2252 GLU, B 2265 GLU, B 2268 ALA, B 2289 LYS, B 2313 GLU, B 2314 GLU HAVE NO ELECTRON DENSITY BUT THEY WERE MODELED. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2239 HIS, A 2240 LYS, A 2242 ARG, A 2250 ARG, A 2252 GLU, A 2268 ALA, A 2286 GLU, A 2314 GLU, B 2240 LYS, B 2250 ARG, B 2286 GLU, B 2306 GLU HAVE A POORLY DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 895 5.1 %RANDOM
Rwork0.209 ---
obs0.21 16730 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 10 70 1510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9612031
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.08824.06264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18615218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.021159
X-RAY DIFFRACTIONr_chiral_restr0.1430.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021170
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.2557
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2956
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4371.5990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33521551
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4473575
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5394.5480
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 655 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.350.5
2Bmedium positional0.350.5
1Amedium thermal1.842
2Bmedium thermal1.842
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 68
Rwork0.233 1208

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