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- PDB-1wxa: Solution Structure of Ras-binding Domain in Mouse AF-6 Protein -

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Basic information

Entry
Database: PDB / ID: 1wxa
TitleSolution Structure of Ras-binding Domain in Mouse AF-6 Protein
ComponentsAfadin
KeywordsCELL ADHESION / Ras-binding domain / ubiquitin-like fold / AF-6 protein / Structural genomics / Afadin / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / protein localization to cell junction / Adherens junctions interactions / dendrite arborization / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion ...regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / protein localization to cell junction / Adherens junctions interactions / dendrite arborization / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / pore complex assembly / LIM domain binding / cell-cell adhesion mediated by cadherin / telencephalon development / neuroepithelial cell differentiation / positive regulation of dendritic spine morphogenesis / bicellular tight junction assembly / cell-cell contact zone / positive regulation of dendrite extension / brain morphogenesis / positive regulation of mini excitatory postsynaptic potential / tight junction / positive regulation of dendrite morphogenesis / apical junction complex / pore complex / homeostasis of number of cells / somatodendritic compartment / cell adhesion molecule binding / negative regulation of cell migration / adherens junction / cerebral cortex development / small GTPase binding / regulation of protein localization / actin filament binding / cell-cell junction / apical part of cell / cell junction / nuclear speck / axon / positive regulation of gene expression / signal transduction / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhao, C. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of Ras-binding Domain in Mouse AF-6 Protein
Authors: Zhao, C. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionJan 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Afadin


Theoretical massNumber of molelcules
Total (without water)12,6131
Polymers12,6131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Afadin / / Af-6 protein


Mass: 12613.141 Da / Num. of mol.: 1 / Fragment: Ras-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free synthesis / Gene: RIKEN cDNA 4932441D06 / Plasmid: P040719-08 / References: UniProt: Q9QZQ1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.28mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298.0 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.921Kobayashi, N.data analysis
CYANA1.0.8Guentert, P.structure solution
CYANA1.0.8Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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