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- PDB-2k7q: Filamin A Ig-like domains 18-19 -

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Basic information

Entry
Database: PDB / ID: 2k7q
TitleFilamin A Ig-like domains 18-19
ComponentsFilamin-A
KeywordsSTRUCTURAL PROTEIN / filamin / Ig-like / ABP-280 / actin binding protein / Acetylation / Actin-binding / Cytoplasm / Cytoskeleton / Disease mutation / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


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 / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation ...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 / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / 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 / 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 / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / positive regulation of axon regeneration / receptor clustering / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / brush border / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / small GTPase binding / kinase binding / platelet aggregation / Z disc / positive regulation of protein import into nucleus / cell-cell junction / actin filament binding / actin cytoskeleton / Platelet degranulation / GTPase binding / negative regulation of neuron projection development / actin cytoskeleton organization / postsynapse / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / protein stabilization / cadherin binding / focal adhesion / glutamatergic synapse / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / 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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...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 / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsHeikkinen, O.K. / Kilpelainen, I. / Koskela, H. / Permi, P. / Heikkinen, S. / Ylanne, J.
Citation
Journal: J Biol Chem / Year: 2009
Title: Atomic structures of two novel immunoglobulin-like domain pairs in the actin cross-linking protein filamin.
Authors: Outi K Heikkinen / Salla Ruskamo / Peter V Konarev / Dmitri I Svergun / Tatu Iivanainen / Sami M Heikkinen / Perttu Permi / Harri Koskela / Ilkka Kilpeläinen / Jari Ylänne /
Abstract: Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain and 24 immunoglobulin-like domains (IgFLNs). Filamins interact with numerous proteins, including the ...Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain and 24 immunoglobulin-like domains (IgFLNs). Filamins interact with numerous proteins, including the cytoplasmic domains of plasma membrane signaling and cell adhesion receptors. Thereby filamins mechanically and functionally link the cell membrane to the cytoskeleton. Most of the interactions have been mapped to the C-terminal IgFLNs 16-24. Similarly, as with the previously known compact domain pair of IgFLNa20-21, the two-domain fragments IgFLNa16-17 and IgFLNa18-19 were more compact in small angle x-ray scattering analysis than would be expected for two independent domains. Solution state NMR structures revealed that the domain packing in IgFLNa18-19 resembles the structure of IgFLNa20-21. In both domain pairs the integrin-binding site is masked, although the details of the domain-domain interaction are partly distinct. The structure of IgFLNa16-17 revealed a new domain packing mode where the adhesion receptor binding site of domain 17 is not masked. Sequence comparison suggests that similar packing of three tandem filamin domain pairs is present throughout the animal kingdom, and we propose that this packing is involved in the regulation of filamin interactions through a mechanosensor mechanism.
#1: Journal: To be Published
Title: 1H,13C,15N chemical shift assignments for filamin A Ig-like domain pairs 16-17 and 18-19
Authors: Heikkinen, O. / Koskela, H. / Permi, P. / Heikkinen, S. / Kilpelainen, I. / Ylanne, J.
History
DepositionAug 19, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Filamin-A


Theoretical massNumber of molelcules
Total (without water)20,4061
Polymers20,4061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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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 / Non-muscle filamin


Mass: 20405.945 Da / Num. of mol.: 1 / Fragment: Filamin 18-19, UNP residues 1954-2141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21333

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C-CT-HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCA
1613D HN(CA)CB
1713D H(CCO)NH
1813D (H)CCH-COSY
1913D 1H-13C NOESY
11013D 1H-15N NOESY
11112D 1H-13C-CT-HSQC aromatics
11212D (HB)CB(CGCDCE)HE
11312D (HB)CB(CGCD)HD
11413D HN(CO)CA
11513D HNCO
11613D (H)CCH-TOCSY
1171HN(CA)CO
1181HNCAHA

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Sample preparation

DetailsContents: 0.8mM [U-13C; U-15N] FLNa18-19, 50mM sodium phosphate, 100mM potassium chloride, 1mM DTT, 2mM sodium azide, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMFLNa18-19[U-13C; U-15N]1
50 mMsodium phosphate1
100 mMpotassium chloride1
1 mMDTT1
2 mMsodium azide1
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
VnmrJVarianprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: implicit Born solvent model
NMR constraintsNOE constraints total: 2930 / NOE long range total count: 1467 / NOE medium range total count: 331 / Protein phi angle constraints total count: 117 / Protein psi angle constraints total count: 117
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 14.22 ° / Maximum upper distance constraint violation: 0.22 Å / Representative conformer: 19

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