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- PDB-1x5r: Solution structure of the fourth PDZ domain of Glutamate receptor... -

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Basic information

Entry
Database: PDB / ID: 1x5r
TitleSolution structure of the fourth PDZ domain of Glutamate receptor interacting protein 2
ComponentsGlutamate receptor interacting protein 2
KeywordsSIGNALING PROTEIN / PDZ domain / Glutamate receptor interacting protein 2 / GRIP2 protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Trafficking of GluR2-containing AMPA receptors / vesicle-mediated transport in synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / artery smooth muscle contraction / neuron spine / positive regulation of blood pressure / postsynaptic density, intracellular component / glutamate receptor binding / Notch signaling pathway / postsynaptic membrane ...Trafficking of GluR2-containing AMPA receptors / vesicle-mediated transport in synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / artery smooth muscle contraction / neuron spine / positive regulation of blood pressure / postsynaptic density, intracellular component / glutamate receptor binding / Notch signaling pathway / postsynaptic membrane / neuronal cell body / dendrite / glutamatergic synapse / plasma membrane / cytosol
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the fourth PDZ domain of Glutamate receptor interacting protein 2
Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 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: Glutamate receptor interacting protein 2


Theoretical massNumber of molelcules
Total (without water)11,4501
Polymers11,4501
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 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Glutamate receptor interacting protein 2 / GRIP2 protein


Mass: 11449.641 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 pf00330s1 / Plasmid: P040705-16 / References: UniProt: Q9C0E4

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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
NMR detailsText: spectrometer_id 1 for 3D_15N_separated_NOESY; spectrometer_id 2 for 3D_13C_separated_NOESY

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Sample preparation

DetailsContents: 0.95mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9296Kobayashi,N.data analysis
CYANA1.0.7Guntert,P.structure solution
CYANA1.0.7Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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