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- PDB-2jf1: CRYSTAL STRUCTURE OF THE FILAMIN A REPEAT 21 COMPLEXED WITH THE I... -

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Basic information

Entry
Database: PDB / ID: 2jf1
TitleCRYSTAL STRUCTURE OF THE FILAMIN A REPEAT 21 COMPLEXED WITH THE INTEGRIN BETA2 CYTOPLASMIC TAIL PEPTIDE
Components
  • FILAMIN-A
  • INTEGRIN BETA-2 SUBUNIT
KeywordsCELL ADHESION / ACTIN-BINDING / TRANSMEMBRANE / ACETYLATION / POLYMORPHISM / CYTOSKELETON / GLYCOPROTEIN / FILAMIN / COMPLEX / MEMBRANE / INTEGRIN / RECEPTOR / PYRROLIDONE CARBOXYLIC ACID / PHOSPHORYLATION / DISEASE MUTATION / IMMUNOGLOBULIN LIKE
Function / homology
Function and homology information


integrin alphaD-beta2 complex / integrin alphaX-beta2 complex / 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 / cellular extravasation / integrin alphaM-beta2 complex / glycoprotein Ib-IX-V complex / positive regulation of neutrophil degranulation ...integrin alphaD-beta2 complex / integrin alphaX-beta2 complex / 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 / cellular extravasation / integrin alphaM-beta2 complex / glycoprotein Ib-IX-V complex / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / ICAM-3 receptor activity / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / blood coagulation, intrinsic pathway / tubulin deacetylation / OAS antiviral response / leukocyte migration involved in inflammatory response / actin crosslink formation / complement component C3b binding / positive regulation of actin filament bundle assembly / Toll Like Receptor 4 (TLR4) Cascade / : / positive regulation of neuron migration / neutrophil migration / protein localization to bicellular tight junction / Cell-extracellular matrix interactions / positive regulation of potassium ion transmembrane transport / positive regulation of platelet activation / apical dendrite / positive regulation of neural precursor cell proliferation / Fc-gamma receptor I complex binding / podosome / protein localization to cell surface / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / negative regulation of transcription by RNA polymerase I / cell adhesion mediated by integrin / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / phagocytosis, engulfment / megakaryocyte development / GP1b-IX-V activation signalling / leukocyte cell-cell adhesion / negative regulation of dopamine metabolic process / SMAD binding / receptor clustering / endodermal cell differentiation / cortical cytoskeleton / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / amyloid-beta clearance / tertiary granule membrane / ficolin-1-rich granule membrane / cilium assembly / : / mitotic spindle assembly / plasma membrane raft / positive regulation of protein targeting to membrane / Integrin cell surface interactions / potassium channel regulator activity / cellular response to low-density lipoprotein particle stimulus / endothelial cell migration / specific granule membrane / positive regulation of superoxide anion generation / heat shock protein binding / release of sequestered calcium ion into cytosol / neutrophil chemotaxis / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / regulation of cell migration / receptor-mediated endocytosis / cell-matrix adhesion / dendritic shaft / Cell surface interactions at the vascular wall / integrin-mediated signaling pathway / protein localization to plasma membrane / actin filament / establishment of protein localization / protein sequestering activity / microglial cell activation / cell-cell adhesion / negative regulation of protein catabolic process / cerebral cortex development / positive regulation of protein import into nucleus / receptor internalization / G protein-coupled receptor binding / mRNA transcription by RNA polymerase II / platelet aggregation / integrin binding / small GTPase binding / Z disc / kinase binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / cell-cell junction / actin filament binding
Similarity search - Function
Integrin beta-2 subunit / 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 ...Integrin beta-2 subunit / 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 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Calponin homology domain / Calponin homology (CH) domain / Integrin domain superfamily / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrin beta-2 / Filamin-A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKiema, T. / Ylanne, J.
CitationJournal: Blood / Year: 2008
Title: Beta2 Integrin Phosphorylation on Thr758 Acts as a Molecular Switch to Regulate 14-3-3 and Filamin Binding.
Authors: Takala, H. / Nurminen, E. / Nurmi, S.M. / Aatonen, M. / Strandin, T. / Takatalo, M. / Kiema, T. / Gahmberg, C.G. / Ylanne, J. / Fagerholm, S.C.
History
DepositionJan 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 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 / 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
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
T: INTEGRIN BETA-2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2713
Polymers14,1792
Non-polymers921
Water34219
1
A: FILAMIN-A
T: INTEGRIN BETA-2 SUBUNIT
hetero molecules

A: FILAMIN-A
T: INTEGRIN BETA-2 SUBUNIT
hetero molecules

A: FILAMIN-A
T: INTEGRIN BETA-2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8139
Polymers42,5366
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6930 Å2
ΔGint-49 kcal/mol
Surface area17120 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.720, 78.720, 78.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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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: 9964.994 Da / Num. of mol.: 1 / Fragment: IG 21, RESIDUES 2236-2329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21333
#2: Protein/peptide INTEGRIN BETA-2 SUBUNIT / CELL SURFACE ADHESION GLYCOPROTEINS LFA-1/CR3/P150 / 95 SUBUNIT BETA / COMPLEMENT RECEPTOR C3 ...CELL SURFACE ADHESION GLYCOPROTEINS LFA-1/CR3/P150 / 95 SUBUNIT BETA / COMPLEMENT RECEPTOR C3 SUBUNIT BETA / CD18 ANTIGEN


Mass: 4213.747 Da / Num. of mol.: 1 / Fragment: RESIDUES 735-769 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05107
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.91 Å3/Da / Density % sol: 68.32 % / Description: NONE
Crystal growpH: 4.6
Details: 1.6-1.58 M AMMONIUM SULPHATE, 0.1 M NA-ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→45.46 Å / Num. obs: 8482 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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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

2brq


Resolution: 2.2→45.45 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.77 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 849 10 %RANDOM
Rwork0.247 ---
obs0.25 7633 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 6 19 742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022738
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9641000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85424.48329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.7615105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.931153
X-RAY DIFFRACTIONr_chiral_restr0.1270.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2239
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2451.5491
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1552773
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1953272
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4684.5227
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
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 62 -
Rwork0.302 555 -
obs--100 %

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