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- PDB-2g5m: Spinophilin PDZ domain -

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Basic information

Entry
Database: PDB / ID: 2g5m
TitleSpinophilin PDZ domain
ComponentsNeurabin-2
KeywordsPROTEIN BINDING / Spinophilin / PDZ domain / CNS / synaptic transmission
Function / homology
Function and homology information


protein localization to actin cytoskeleton / positive regulation of protein localization to actin cortical patch / response to L-phenylalanine derivative / cytoplasmic side of dendritic spine plasma membrane / regulation of opioid receptor signaling pathway / protein localization to cell periphery / cellular response to morphine / developmental process involved in reproduction / response to prostaglandin E / response to kainic acid ...protein localization to actin cytoskeleton / positive regulation of protein localization to actin cortical patch / response to L-phenylalanine derivative / cytoplasmic side of dendritic spine plasma membrane / regulation of opioid receptor signaling pathway / protein localization to cell periphery / cellular response to morphine / developmental process involved in reproduction / response to prostaglandin E / response to kainic acid / reproductive system development / cellular response to peptide / protein phosphatase 1 binding / filopodium assembly / actin filament depolymerization / dendritic spine membrane / response to steroid hormone / protein phosphatase inhibitor activity / positive regulation of protein localization / male mating behavior / cortical actin cytoskeleton / dendritic spine neck / dendritic spine head / dendrite development / response to immobilization stress / cellular response to organic cyclic compound / response to amino acid / D2 dopamine receptor binding / cellular response to epidermal growth factor stimulus / response to amphetamine / response to organonitrogen compound / response to nicotine / filopodium / learning / actin filament organization / cellular response to estradiol stimulus / calcium-mediated signaling / hippocampus development / positive regulation of protein localization to plasma membrane / adherens junction / regulation of protein phosphorylation / negative regulation of cell growth / response to organic cyclic compound / cerebral cortex development / ruffle membrane / kinase binding / neuron projection development / cell migration / actin filament binding / cellular response to xenobiotic stimulus / actin cytoskeleton / response to estradiol / lamellipodium / actin binding / growth cone / transmembrane transporter binding / dendritic spine / postsynaptic density / nucleic acid binding / protein kinase activity / response to xenobiotic stimulus / neuronal cell body / dendrite / protein-containing complex binding / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / 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 ...Neurabin-1/2, PDZ domain / Neurabin-like family / 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
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsKelker, M.S. / Peti, W.
CitationJournal: Biochemistry / Year: 2007
Title: Structural basis for spinophilin-neurabin receptor interaction.
Authors: Kelker, M.S. / Dancheck, B. / Ju, T. / Kessler, R.P. / Hudak, J. / Nairn, A.C. / Peti, W.
History
DepositionFeb 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Neurabin-2


Theoretical massNumber of molelcules
Total (without water)12,1361
Polymers12,1361
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Neurabin-2 / Neurabin-II / Neural tissue-specific F-actin binding protein II / Protein phosphatase 1 regulatory ...Neurabin-II / Neural tissue-specific F-actin binding protein II / Protein phosphatase 1 regulatory subunit 9B / Spinophilin / p130 / PP1bp134


Mass: 12135.745 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r9b / Plasmid: derivitive of pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL codon plus / References: UniProt: O35274

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N resolved [1H,1H] NOESY
1223D 13C resolved [1H,1H] NOESY
1332D 1H-1H NOESY
NMR detailsText: The following spectra were used to achieve the sequence-specific backbone and side chain assignments of all aliphatic residues: 2D [1H,15N]-HSQC, 2D [1H,13C]-HSQC, 3D HNCACB, 3D CBCA(CO)NH, 3D ...Text: The following spectra were used to achieve the sequence-specific backbone and side chain assignments of all aliphatic residues: 2D [1H,15N]-HSQC, 2D [1H,13C]-HSQC, 3D HNCACB, 3D CBCA(CO)NH, 3D CC(CO)NH, 3D HNCO, 3D HNCA, 3D HBHA(CO)NH, 3D 15N-resolved [1H,1H]-TOCSY, 3D HC(C)H-TOCSY6. The 2D [1H,1H]-NOESY, 2D [1H,1H]-TOCSY and 2D [1H,1H]-COSY spectra of the Spinophilin493-602 sample in D2O solution after complete H/D exchange of the labile protons were used for the assignment of the aromatic side chains. The NMR spectra were processed with Topspin1.3, and analyzed with the CARA software package. Spectra used for the structure calculation were: 3D 15N-resolved [1H,1H]-NOESY, 3D 13C-resolved [1H,1H]-NOESY (mixing time of 85 ms) and 2D [1H,1H]-NOESY (mixing time 85 ms, D2O solution).

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM PDZ domain, 15N samples; 20 mM Na phosphate buffer 50 mM NaCl, pH 6.5; 90% H2O, 10% D2O90% H2O/10% D2O
21.8 mM PDZ domain, 13C/15N samples; 20 mM Na phosphate buffer 50 mM NaCl, pH 6.5; 90% H2O, 10% D2O90% H2O/10% D2O
31.8 mM PDZ domain, 13C/15N samples; 20 mM Na phosphate buffer 50 mM NaCl, pH 6.5; 90% H2O, 10% D2O100% d20
Sample conditionsIonic strength: 20 mM Na phosphate; 50 mM NaCl / pH: 6.5 / 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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukerprocessing
CYANA2peter guntertstructure solution
CNS1.1Brungerrefinement
atnos/candid2Torsten Herrmannstructure solution
CARA1.5Rochus Kellerdata analysis
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
Details: The amino acid sequence, the chemical shift assignment, and the NOESY spectra were input for the automated NOESY peak picking and NOE assignment method of ATNOS/CANDID/CYANA. The results of ...Details: The amino acid sequence, the chemical shift assignment, and the NOESY spectra were input for the automated NOESY peak picking and NOE assignment method of ATNOS/CANDID/CYANA. The results of ATNOS/CANDID/CYANA were refined by manual peak adjustment and additional calculations in CYANA. The 20 conformers from the ATNOS/CANDID cycle 7 with the lowest residual CYANA target function values were energy-minimized in a water shell with the program CNS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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