[English] 日本語
Yorodumi
- PDB-3isw: Crystal structure of filamin-A immunoglobulin-like repeat 21 boun... -

+
Open data


ID or keywords:

Loading...

-
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 cyclic nucleotide-gated ion 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 cyclic nucleotide-gated ion channel activity / positive regulation of integrin-mediated signaling pathway / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / cytoplasmic sequestering of protein / positive regulation of enamel mineralization / transepithelial water transport / tubulin deacetylation / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / actin crosslink formation / blood coagulation, intrinsic pathway / amelogenesis / protein localization to bicellular tight junction / chloride channel inhibitor activity / OAS antiviral response / ATPase-coupled inorganic anion transmembrane transporter activity / positive regulation of actin filament bundle assembly / Golgi-associated vesicle membrane / positive regulation of neuron migration / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / multicellular organismal-level water homeostasis / early endosome to late endosome transport / apical dendrite / Fc-gamma receptor I complex binding / cell-cell junction organization / membrane hyperpolarization / cholesterol transport / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle docking involved in exocytosis / chloride channel regulator activity / protein localization to cell surface / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / chloride transmembrane transporter activity / sperm capacitation / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / chloride channel activity / positive regulation of axon regeneration / RHOQ GTPase cycle / receptor clustering / SMAD binding / cholesterol biosynthetic process / positive regulation of exocytosis / RHO GTPases activate PAKs / actin filament bundle / positive regulation of insulin secretion involved in cellular response to glucose stimulus / brush border / chloride channel complex / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / ATPase-coupled transmembrane transporter activity / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / ABC-type transporter activity / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / cellular response to cAMP / cellular response to forskolin / regulation of cell migration / chloride transmembrane transport / isomerase activity / response to endoplasmic reticulum stress / dendritic shaft / establishment of localization in cell / protein localization to plasma membrane / PDZ domain binding / G protein-coupled receptor binding / actin filament / protein kinase C binding / Defective CFTR causes cystic fibrosis / synapse organization / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / mRNA transcription by RNA polymerase II / establishment of protein localization / ABC-family proteins mediated transport / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / recycling endosome
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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more