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- PDB-2brq: Crystal structure of the filamin A repeat 21 complexed with the i... -

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Basic information

Entry
Database: PDB / ID: 2brq
TitleCrystal structure of the filamin A repeat 21 complexed with the integrin beta7 cytoplasmic tail peptide
Components
  • FILAMIN A
  • INTEGRIN BETA-7 SUBUNIT
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON-COMPLEX / ACTIN-BINDING / CYTOSKELETON / IMMUNOGLOBULIN LIKE / INTEGRIN / CELL ADHESION
Function / homology
Function and homology information


immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 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 / glycoprotein Ib-IX-V complex / formation of radial glial scaffolds / T cell migration ...immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 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 / glycoprotein Ib-IX-V complex / formation of radial glial scaffolds / T cell migration / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / tubulin deacetylation / cytoplasmic sequestering of protein / actin crosslink formation / 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 / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / leukocyte tethering or rolling / early endosome to late endosome transport / apical dendrite / Fc-gamma receptor I complex binding / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / heterotypic cell-cell adhesion / integrin complex / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / leukocyte migration / cortical cytoskeleton / positive regulation of axon regeneration / receptor clustering / SMAD binding / actin filament bundle / RHO GTPases activate PAKs / brush border / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / Integrin cell surface interactions / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / cell adhesion molecule binding / regulation of cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / dendritic shaft / protein localization to plasma membrane / integrin-mediated signaling pathway / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / mRNA transcription by RNA polymerase II / trans-Golgi network / establishment of protein localization / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / platelet aggregation / kinase binding / small GTPase binding / cell-cell adhesion / Z disc / positive regulation of protein import into nucleus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin filament binding / cell-cell junction / actin cytoskeleton / integrin binding / negative regulation of neuron projection development / Platelet degranulation / GTPase binding / virus receptor activity / actin cytoskeleton organization / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / postsynapse / receptor complex / protein stabilization / cell adhesion / cadherin binding / focal adhesion / glutamatergic synapse
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta subunit, tail ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / EGF-like domain, extracellular / EGF-like domain / Integrin domain superfamily / Calponin homology domain / Calponin homology (CH) domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLUTATHIONE / Filamin-A / Integrin beta-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKiema, T.-R. / Ylanne, J.
CitationJournal: Mol.Cell / Year: 2006
Title: The Molecular Basis of Filamin Binding to Integrins and Competition with Talin.
Authors: Kiema, T. / Lad, Y. / Jiang, P. / Oxley, C.L. / Baldassarre, M. / Wegener, K.L. / Campbell, I.D. / Ylanne, J. / Calderwood, D.A.
History
DepositionMay 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 29, 2012Group: Other
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_conn / 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_conn.pdbx_leaving_atom_flag / _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.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_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: INTEGRIN BETA-7 SUBUNIT
D: INTEGRIN BETA-7 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8358
Polymers27,0364
Non-polymers7994
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-30 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.970, 60.000, 51.570
Angle α, β, γ (deg.)90.00, 110.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA2236 - 23284 - 96
21GLYGLYBB2236 - 23284 - 96
12PROPROCC776 - 7889 - 21
22PROPRODD776 - 7889 - 21

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.87626, 0.4813, 0.02267), (0.48019, 0.86842, 0.12356), (0.03978, 0.11916, -0.99208)37.53052, -14.52401, 72.62393
2given(-0.89308, 0.44922, 0.02465), (0.44772, 0.88205, 0.14674), (0.04418, 0.14209, -0.98887)38.72989, -14.63607, 72.13455

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Components

#1: Protein FILAMIN A / ALPHA-FILAMIN / FILAMIN 1 / ENDOTHELIAL ACTIN- BINDING PROTEIN / ACTIN-BINDING PROTEIN 280 / ABP- ...ALPHA-FILAMIN / FILAMIN 1 / ENDOTHELIAL ACTIN- BINDING PROTEIN / ACTIN-BINDING PROTEIN 280 / ABP-280 / NONMUSCLE FILAMIN


Mass: 9964.994 Da / Num. of mol.: 2 / Fragment: ROD DOMAIN, 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-7 SUBUNIT


Mass: 3552.918 Da / Num. of mol.: 2 / Fragment: RESIDUES 768-798 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P26010
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLUTATHIONE (GTT): GLUTATHIONES X1 AND X2 ARE COVALENTLY ATTACHED TO A 2293 CYS AND B 2293 CYS, ...GLUTATHIONE (GTT): GLUTATHIONES X1 AND X2 ARE COVALENTLY ATTACHED TO A 2293 CYS AND B 2293 CYS, RESPECTIVELY, FORMING A DISULFIDE BOND.
Sequence detailsTHE FIRST THREE RESIDUES GAM ORIGINATES FROM THE EXPRESSION PLASMID.

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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: 2.6 Å3/Da / Density % sol: 52.6 % / Description: FILAMIN C REPEAT 24
Crystal growpH: 5.5 / Details: 1.26 M SODIUM CITRATE, 0.1 M CITRIC ACID PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Feb 17, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→37.68 Å / Num. obs: 13748 / % possible obs: 96.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V05

1v05


Resolution: 2.1→37.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.227 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2264 ARG, A 2280 LYS, A 2287 ASP, B 2240 LYS, B 2250 ARG, B 2262 TRP, B 2280 LYS, B 2287 ASP, B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2264 ARG, A 2280 LYS, A 2287 ASP, B 2240 LYS, B 2250 ARG, B 2262 TRP, B 2280 LYS, B 2287 ASP, B 2288 ARG, D 785 THR AND D 787 ASN HAVE A POORLY DEFINED DENSITY. THE SIDE CHAIN ATOMS OF RESIDUES A 2289 LYS, B 2239 HIS, B 2264 ARG, B 2286 GLU, B 2289 LYS AND B 2314 GLU HAVE NO ELECTRON DENSITY BUT THEY WERE MODELED. BREAK IN THE MAIN CHAIN ELECTRON DENSITY BETWEEN RESIDUES B 2286 GLU - B 2287 ASP, B 2288 ARG - B 2289 LYS AND D 786 ILE - D 787 ASN.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1381 10 %RANDOM
Rwork0.192 ---
obs0.197 12367 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.65 Å2
2--1.33 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 52 50 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9982238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08124.37564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87615229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.414158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021288
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2595
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21054
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7691.51089
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23621696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0253636
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2234.5542
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A372tight positional0.290.05
12B372tight positional0.290.05
21C52tight positional0.20.05
22D52tight positional0.20.05
11A306loose positional0.725
12B306loose positional0.725
21C48loose positional0.45
22D48loose positional0.45
11A372tight thermal1.360.5
12B372tight thermal1.360.5
21C52tight thermal1.530.5
22D52tight thermal1.530.5
11A306loose thermal1.9710
12B306loose thermal1.9710
21C48loose thermal1.9210
22D48loose thermal1.9210
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 112
Rwork0.224 890
Refinement TLS params.

T33: -0.1593 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
16.27081.33231.50354.33991.54635.569-0.11690.0301-0.1845-0.3916-0.04390.0365-0.1575-0.12030.1608-0.16380.06420.0418-0.2009-0.004930.97416.299926.9218
24.1139-2.25350.86235.9181-2.35167.4417-0.2123-0.6395-0.27050.56010.16930.12670.05610.43110.043-0.16130.05830.0349-0.00830.032318.927717.653549.1184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2236 - 2329
2X-RAY DIFFRACTION1C776 - 788
3X-RAY DIFFRACTION1A3330
4X-RAY DIFFRACTION2B2236 - 2328
5X-RAY DIFFRACTION2D776 - 788
6X-RAY DIFFRACTION2B3329

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