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- PDB-3isw: Crystal structure of filamin-A immunoglobulin-like repeat 21 boun... -

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Basic information

Entry
Database: PDB / ID: 3isw
TitleCrystal structure of filamin-A immunoglobulin-like repeat 21 bound to an N-terminal peptide of CFTR
Components
  • Cystic fibrosis transmembrane conductance regulator
  • Filamin-A
KeywordsSTRUCTURAL PROTEIN / protein-peptide complex / Acetylation / Actin-binding / Alternative splicing / Cytoplasm / Cytoskeleton / Disease mutation / Phosphoprotein / Polymorphism / ATP-binding / Chloride / Chloride channel / Glycoprotein / Hydrolase / Ion transport / Ionic channel / Membrane / Nucleotide-binding / Transmembrane / Transport
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 voltage-gated chloride channel activity / positive regulation of integrin-mediated signaling pathway / : ...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 voltage-gated chloride channel activity / positive regulation of integrin-mediated signaling pathway / : / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / actin crosslink formation / RHO GTPases regulate CFTR trafficking / blood coagulation, intrinsic pathway / tubulin deacetylation / amelogenesis / OAS antiviral response / intracellular pH elevation / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / chloride channel inhibitor activity / : / protein localization to bicellular tight junction / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / Fc-gamma receptor I complex binding / Cell-extracellular matrix interactions / cholesterol transport / apical dendrite / positive regulation of potassium ion transmembrane transport / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / vesicle docking involved in exocytosis / membrane hyperpolarization / protein localization to cell surface / wound healing, spreading of cells / chloride transmembrane transporter activity / podosome / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / sperm capacitation / cholesterol biosynthetic process / SMAD binding / receptor clustering / cortical cytoskeleton / RHOQ GTPase cycle / chloride channel activity / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / positive regulation of exocytosis / cilium assembly / ATPase-coupled transmembrane transporter activity / mitotic spindle assembly / potassium channel regulator activity / chloride channel complex / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / negative regulation of DNA-binding transcription factor activity / 14-3-3 protein binding / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / cellular response to forskolin / protein sequestering activity / regulation of cell migration / chloride transmembrane transport / response to endoplasmic reticulum stress / cellular response to cAMP / dendritic shaft / protein localization to plasma membrane / actin filament / PDZ domain binding / establishment of protein localization / establishment of localization in cell / clathrin-coated endocytic vesicle membrane / mRNA transcription by RNA polymerase II / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / G protein-coupled receptor binding / recycling endosome / cerebral cortex development / negative regulation of protein catabolic process / ABC-family proteins mediated transport / positive regulation of protein import into nucleus / small GTPase binding / transmembrane transport / platelet aggregation / kinase binding / Z disc / recycling endosome membrane / Chaperone Mediated Autophagy / Aggrephagy / actin filament binding
Similarity search - Function
Filamin family / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like ...Filamin family / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / 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. / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin E-set / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Cystic fibrosis transmembrane conductance regulator / Filamin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXu, Z. / Page, R. / Qin, J. / Ithychanda, S.S. / Liu, J.M. / Misra, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Biochemical basis of the interaction between cystic fibrosis transmembrane conductance regulator and immunoglobulin-like repeats of filamin.
Authors: Smith, L. / Page, R.C. / Xu, Z. / Kohli, E. / Litman, P. / Nix, J.C. / Ithychanda, S.S. / Liu, J. / Qin, J. / Misra, S. / Liedtke, C.M.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamin-A
B: Filamin-A
C: Cystic fibrosis transmembrane conductance regulator


Theoretical massNumber of molelcules
Total (without water)22,3643
Polymers22,3643
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-14.2 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.152, 74.152, 289.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsTHE BIOLOGICAL ASSEMBLY IS THE DIMERIC COMPLEX OF THE PROTEIN WITH THE PEPTIDE, REPRESENTED BY THE ENTIRE CONTENTS OF THE ASYMMETRIC UNIT. THE SOFTWARE-GENERATED WORD 'TRIMERIC' IN REMARK 350 IS A POLYMERIC COUNT.

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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: 10177.196 Da / Num. of mol.: 2 / Fragment: UNP residues 2236-2329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLN, FLN-21, FLN1, FLNA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P21333
#2: Protein/peptide Cystic fibrosis transmembrane conductance regulator / CFTR / Channel conductance-controlling ATPase / cAMP-dependent chloride channel / ATP-binding ...CFTR / Channel conductance-controlling ATPase / cAMP-dependent chloride channel / ATP-binding cassette transporter sub-family C member 7


Mass: 2009.345 Da / Num. of mol.: 1 / Fragment: UNP residues 5-22 / Mutation: R21A / Source method: obtained synthetically
Details: Synthetic peptide based on the sequence 5-22 of Homo sapiens CFTR (UniProt entry P13569, CFTR_HUMAN)
References: UniProt: P13569
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.13 Å3/Da / Density % sol: 76.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-Tris Propane pH 7.0, 60% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 1, 2007
Details: ROSENBAUM-ROCK MONOCHROMATOR FOR SAGITAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→42.97 Å / Num. all: 13108 / Num. obs: 12452 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 8.53 % / Biso Wilson estimate: 75.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Χ2: 0.94 / Net I/σ(I): 13.8 / Scaling rejects: 3169
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.41 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1177 / Rsym value: 0.472 / Χ2: 1.34 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.7LDzdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BRQ

2brq


Resolution: 2.8→34.73 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.066 / SU ML: 0.277 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.403 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 580 4.8 %RANDOM
Rwork0.263 ---
all0.264 12007 --
obs0.264 12007 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 69.191 Å2 / Biso min: 37.96 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å22.36 Å20 Å2
2--4.72 Å20 Å2
3----7.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 0 14 1518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221543
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.962095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5895202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12124.21964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.37615220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.752158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021212
X-RAY DIFFRACTIONr_nbd_refined0.240.2552
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.22
X-RAY DIFFRACTIONr_mcbond_it1.031.51029
X-RAY DIFFRACTIONr_mcangle_it1.85321615
X-RAY DIFFRACTIONr_scbond_it1.9943574
X-RAY DIFFRACTIONr_scangle_it3.5194.5480
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 46 -
Rwork0.379 829 -
all-875 -
obs-829 98.43 %

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