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- PDB-1ujv: Solution structure of the second PDZ domain of human membrane ass... -

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Basic information

Entry
Database: PDB / ID: 1ujv
TitleSolution structure of the second PDZ domain of human membrane associated guanylate kinase inverted-2 (MAGI-2)
ComponentsMEMBRANE ASSOCIATED GUANYLATE KINASE INVERTED-2 (MAGI-2)
KeywordsSIGNALING PROTEIN / atrophin-1 interacting protein 1 / PDZ domain / structural genomics / KIAA0705 protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / type II activin receptor binding / podocyte development / slit diaphragm / beta-1 adrenergic receptor binding / nerve growth factor signaling pathway / clathrin-dependent endocytosis / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / Nephrin family interactions ...: / type II activin receptor binding / podocyte development / slit diaphragm / beta-1 adrenergic receptor binding / nerve growth factor signaling pathway / clathrin-dependent endocytosis / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / Nephrin family interactions / ciliary base / receptor clustering / positive regulation of receptor internalization / SMAD binding / : / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / photoreceptor outer segment / bicellular tight junction / phosphatase binding / centriole / photoreceptor inner segment / cellular response to nerve growth factor stimulus / negative regulation of cell migration / positive regulation of neuron projection development / cell-cell junction / late endosome / signaling receptor complex adaptor activity / nervous system development / postsynaptic density / negative regulation of cell population proliferation / centrosome / dendrite / synapse / perinuclear region of cytoplasm / signal transduction / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Unstructured region on MAGI / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. ...Unstructured region on MAGI / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. / PDZ domain / Pdz3 Domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsNameki, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the second PDZ domain of human membrane associated guanylate kinase inverted-2 (MAGI-2)
Authors: Nameki, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionAug 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: author determined

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Structure visualization

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Assembly

Deposited unit
A: MEMBRANE ASSOCIATED GUANYLATE KINASE INVERTED-2 (MAGI-2)


Theoretical massNumber of molelcules
Total (without water)9,9161
Polymers9,9161
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein MEMBRANE ASSOCIATED GUANYLATE KINASE INVERTED-2 (MAGI-2) / KIAA0705 PROTEIN


Mass: 9916.074 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA hg03359 / Plasmid: P021030-28 / References: UniProt: Q86UL8

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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

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Sample preparation

DetailsContents: 1.3mM PDZ domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7 / Pressure: ambient / Temperature: 298 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
KUJIRA0.811Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
OPALpKoradi, R., Billeter, M., Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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