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- PDB-5xr1: Structure of FLN IG21 domain in complex with C-terminal peptide o... -

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Basic information

Entry
Database: PDB / ID: 5xr1
TitleStructure of FLN IG21 domain in complex with C-terminal peptide of beta-2
ComponentsC-terminal peptide of Integrin beta-2,Filamin-A IG21 domain
KeywordsSIGNALING PROTEIN / Integrin / cytosolic tail
Function / homology
Function and homology information


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 / cellular extravasation / positive regulation of neutrophil degranulation / establishment of Sertoli cell barrier / integrin alphaM-beta2 complex / Myb complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity ...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 / cellular extravasation / positive regulation of neutrophil degranulation / establishment of Sertoli cell barrier / integrin alphaM-beta2 complex / Myb complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / OAS antiviral response / negative regulation of dopamine metabolic process / positive regulation of actin filament bundle assembly / Toll Like Receptor 4 (TLR4) Cascade / neutrophil migration / positive regulation of neuron migration / leukocyte migration involved in inflammatory response / 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 / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / wound healing, spreading of cells / heterotypic cell-cell adhesion / podosome / negative regulation of transcription by RNA polymerase I / regulation of peptidyl-tyrosine phosphorylation / megakaryocyte development / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / GP1b-IX-V activation signalling / receptor clustering / positive regulation of axon regeneration / cortical cytoskeleton / SMAD binding / endodermal cell differentiation / RHO GTPases activate PAKs / actin filament bundle / amyloid-beta clearance / brush border / semaphorin-plexin signaling pathway / tertiary granule membrane / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / plasma membrane raft / cilium assembly / blood vessel remodeling / positive regulation of protein targeting to membrane / mitotic spindle assembly / epithelial to mesenchymal transition / Integrin cell surface interactions / endothelial cell migration / potassium channel regulator activity / axonal growth cone / heart morphogenesis / specific granule membrane / cell adhesion molecule binding / heat shock protein binding / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / neutrophil chemotaxis / receptor-mediated endocytosis / protein sequestering activity / regulation of cell migration / dendritic shaft / positive regulation of superoxide anion generation / protein kinase C binding / cell-matrix adhesion / protein localization to plasma membrane / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / actin filament / negative regulation of DNA-binding transcription factor activity / trans-Golgi network / microglial cell activation / 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 / cell-cell adhesion / small GTPase 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 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt ...Integrin beta-2 subunit / 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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Integrin beta tail domain / 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 / Integrin domain superfamily / Calponin homology (CH) domain / 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)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChatterjee, D. / Lu, L.Z. / Bhattacharjya, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of EducationARC18/13 Singapore
CitationJournal: To Be Published
Title: Structure of FLN IG21 domain in complex with C-terminal peptide of beta-2
Authors: Chatterjee, D. / Lu, L.Z. / Bhattachrjya, S.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-terminal peptide of Integrin beta-2,Filamin-A IG21 domain


Theoretical massNumber of molelcules
Total (without water)13,7571
Polymers13,7571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein C-terminal peptide of Integrin beta-2,Filamin-A IG21 domain / 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 / FLN-A / Actin-binding protein 280 / ABP-280 / Alpha-filamin / Endothelial actin-binding protein / Filamin-1 / Non-muscle filamin


Mass: 13757.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion protein of C-terminal peptide of Integrin beta-2 (residues 752-763, P05107 (ITB2_HUMAN)), and Filamin-A IG21 domain (residues 2228-2321, P21333 (FLNA_HUMAN)).
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7, FLNA, FLN, FLN1
Production host: BAC cloning vector attB-P[acman]-ApR-F-2-5-attB (others)
References: UniProt: P05107, UniProt: P21333

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY
161isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] FLN IG21 domain, 90% H2O/10% D2O
Label: 15N, 13C_ / Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: FLN IG21 domain / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: Uniformaly 13C, 15N labeled / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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