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- PDB-1t2m: Solution Structure Of The Pdz Domain Of AF-6 -

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Basic information

Entry
Database: PDB / ID: 1t2m
TitleSolution Structure Of The Pdz Domain Of AF-6
ComponentsAF-6 protein
KeywordsPROTEIN BINDING / Chromosomal translocation / Proto-oncogene
Function / homology
Function and homology information


positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / pore complex assembly / cell-cell adhesion mediated by cadherin / bicellular tight junction assembly / cell-cell contact zone / Adherens junctions interactions / tight junction ...positive regulation of cell-cell adhesion mediated by cadherin / establishment of protein localization to plasma membrane / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / pore complex assembly / cell-cell adhesion mediated by cadherin / bicellular tight junction assembly / cell-cell contact zone / Adherens junctions interactions / tight junction / pore complex / cell adhesion molecule binding / negative regulation of cell migration / adherens junction / small GTPase binding / regulation of protein localization / actin filament binding / cell-cell junction / cell junction / cell-cell signaling / cell adhesion / nuclear speck / cadherin binding / positive regulation of gene expression / signal transduction / nucleoplasm / plasma membrane / cytosol
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 / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsZhou, H. / Wu, J.H. / Xu, Y.Q. / Huang, A.D. / Shi, Y.Y.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Solution Structure of AF-6 PDZ Domain and Its Interaction with the C-terminal Peptides from Neurexin and Bcr
Authors: Zhou, H. / Xu, Y. / Yang, Y. / Huang, A. / Wu, J. / Shi, Y.
History
DepositionApr 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 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_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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AF-6 protein


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein AF-6 protein


Mass: 10637.198 Da / Num. of mol.: 1 / Fragment: Pdz domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55196

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 50mM phosphate buffer NA; 1mM EDTA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate, 1mM EDTA / pH: 5.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F. Delaglioprocessing
CNS1.1A.T. Brungerstructure solution
CNS1.1refinement
MOLMOL2K.2Reto Koradidata analysis
Sparky3T.D. Goddardprocessing
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structure was also refined with CSI version 1.0 (authors: David S. Wishart)
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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