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- PDB-1v5q: Solution Structure of the PDZ Domain from Mouse Glutamate Recepto... -

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Basic information

Entry
Database: PDB / ID: 1v5q
TitleSolution Structure of the PDZ Domain from Mouse Glutamate Receptor Interacting Protein 1A-L (GRIP1) Homolog
ComponentsGlutamate Receptor Interacting Protein 1A-L Homolog
KeywordsPROTEIN BINDING / PDZ domain / cellular signaling / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


vesicle-mediated transport in synapse / Trafficking of GluR2-containing AMPA receptors / : / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / nuclear glucocorticoid receptor binding / dendrite development / protein localization / protein transport / signaling receptor complex adaptor activity ...vesicle-mediated transport in synapse / Trafficking of GluR2-containing AMPA receptors / : / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / nuclear glucocorticoid receptor binding / dendrite development / protein localization / protein transport / signaling receptor complex adaptor activity / nervous system development / cytoplasmic vesicle / postsynapse / postsynaptic membrane / perikaryon / postsynaptic density / neuron projection / membrane raft / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Glutamate receptor-interacting protein 1 / Glutamate receptor-interacting protein 1/2 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Glutamate receptor-interacting protein 1 / Glutamate receptor-interacting protein 1/2 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
: / Glutamate receptor-interacting protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the PDZ Domain from Mouse Glutamate Receptor Interacting Protein 1A-L (GRIP1) Homolog
Authors: Sato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionNov 25, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate Receptor Interacting Protein 1A-L Homolog


Theoretical massNumber of molelcules
Total (without water)12,4941
Polymers12,4941
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,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Glutamate Receptor Interacting Protein 1A-L Homolog / GRIP1 Homolog


Mass: 12493.596 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 4931400F03 / Plasmid: P030203-74 / References: GenBank: 26325828, UniProt: Q925T6*PLUS

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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: 0.59mM PDZ domain U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / 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
KUJIRA0.863Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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