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- PDB-1m5z: The PDZ7 of Glutamate Receptor Interacting Protein Binds to its T... -

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Basic information

Entry
Database: PDB / ID: 1m5z
TitleThe PDZ7 of Glutamate Receptor Interacting Protein Binds to its Target via a Novel Hydrophobic Surface Area
ComponentsAMPA receptor interacting protein
KeywordsPROTEIN BINDING / six beta-strands and two alpha-helices
Function / homology
Function and homology information


regulation of synaptic scaling / exocyst / dendrite arborization / vesicle-mediated transport in synapse / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / proximal dendrite / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / spine synapse ...regulation of synaptic scaling / exocyst / dendrite arborization / vesicle-mediated transport in synapse / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / proximal dendrite / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / spine synapse / dendritic spine neck / dendritic spine head / presynaptic active zone / Trafficking of GluR2-containing AMPA receptors / synaptic cleft / GABA-ergic synapse / cellular response to brain-derived neurotrophic factor stimulus / ionotropic glutamate receptor binding / dendritic shaft / synaptic membrane / PDZ domain binding / positive regulation of protein localization to plasma membrane / terminal bouton / recycling endosome / cerebral cortex development / protein localization / GTPase binding / presynapse / presynaptic membrane / nervous system development / perikaryon / postsynaptic membrane / microtubule / postsynapse / dendritic spine / postsynaptic density / neuron projection / membrane raft / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / plasma membrane
Similarity search - Function
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 ...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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFeng, W. / Fan, J. / Jiang, M. / Shi, Y. / Zhang, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The PDZ7 of Glutamate Receptor Interacting Protein Binds to its Target via a Novel Hydrophobic Surface Area
Authors: Feng, W. / Fan, J.-S. / Jiang, M. / Shi, Y.-W. / Zhang, M.
History
DepositionJul 11, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: AMPA receptor interacting protein


Theoretical massNumber of molelcules
Total (without water)9,9791
Polymers9,9791
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 / 200structures with the lowest energy
RepresentativeModel #11closest to the average

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Components

#1: Protein AMPA receptor interacting protein / GRIP


Mass: 9979.455 Da / Num. of mol.: 1
Fragment: The Seventh PDZ Domain of Glutamate Receptor Interacting Protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P97879

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2213D 15N-separated NOESY
3313D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM unlabelled PDZ7 in 99.9% D2O99.9% D2O
21.0 mM 15N-labelled protein in 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM 15N/13C-labelled samples in 99.9% D2O99.9% D2O
41.0 mM 15N/13C-labelled samples in 90% H2O/10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM potassium phosphate buffer / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1826 restraints, 1644 are NOE-derived distance constraints, 126 dihedral angle restraints, 56 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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