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- PDB-1p1d: Structural Insights into the Inter-domain Chaperoning of Tandem P... -

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Basic information

Entry
Database: PDB / ID: 1p1d
TitleStructural Insights into the Inter-domain Chaperoning of Tandem PDZ Domains in Glutamate Receptor Interacting Proteins
ComponentsGlutamate receptor interacting protein
KeywordsPROTEIN BINDING / PDZ domain / Glutamate Receptor / tandem repeats / scaffold protein
Function / homology
Function and homology information


regulation of synaptic scaling / exocyst / vesicle-mediated transport in synapse / dendrite arborization / proximal dendrite / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / cellular response to phorbol 13-acetate 12-myristate / positive regulation of dendrite morphogenesis / spine synapse ...regulation of synaptic scaling / exocyst / vesicle-mediated transport in synapse / dendrite arborization / proximal dendrite / positive regulation of neuron projection arborization / neurotransmitter receptor transport, endosome to postsynaptic membrane / 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 / GABA-ergic synapse / synaptic cleft / cellular response to brain-derived neurotrophic factor stimulus / dendritic shaft / synaptic membrane / PDZ domain binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / protein localization / terminal bouton / recycling endosome / cerebral cortex development / presynapse / GTPase binding / presynaptic membrane / nervous system development / postsynapse / postsynaptic membrane / perikaryon / microtubule / 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
Model type detailsminimized average
AuthorsFeng, W. / Shi, Y. / Li, M. / Zhang, M.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Tandem PDZ repeats in glutamate receptor-interacting proteins have a novel mode of PDZ domain-mediated target binding
Authors: Feng, W. / Shi, Y. / Li, M. / Zhang, M.
History
DepositionApr 12, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: Glutamate receptor interacting protein


Theoretical massNumber of molelcules
Total (without water)21,1931
Polymers21,1931
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 #11minimized average structure

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Components

#1: Protein Glutamate receptor interacting protein / PDZ45


Mass: 21192.941 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-213
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
1223D 15N-separated NOESY
1333D 13C-separated NOESY
144HNCO, HNCA, HN(CO)CA, HN(CA)CB, and HN(COCA)CB
1553D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM unlabelled PDZ45; 100mM phosphate buffer99.9% D2O
21.5mM uniformly 15N labelled PDZ45; 100mM phosphate buffer90% H2O/10% D2O
31.5mM uniformly 15N/13C labelled PDZ45; 100mM phosphate buffer99.9% D2O
41.5mM 80% deuterated, uniformly 13C-/15N-labeled PDZ45; 100mM phosphate buffer90% H2O/10% D2O
51.5mM 100% 2H, 15N-labeled PDZ45; 100mM phosphate buffer90% H2O/10% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 7.0 / Pressure: 1 atm / Temperature: 303 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
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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