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- PDB-7nrn: NMR structure of GIPC1-GH2 domain -

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Basic information

Entry
Database: PDB / ID: 7nrn
TitleNMR structure of GIPC1-GH2 domain
ComponentsPDZ domain-containing protein GIPC1
KeywordsENDOCYTOSIS / ALPHA-HELICAL BUNDLE / PROTEIN BINDING
Function / homology
Function and homology information


FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / positive regulation of melanin biosynthetic process / vesicle membrane / glutamate secretion / cellular response to interleukin-7 / myosin binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / brush border ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / positive regulation of melanin biosynthetic process / vesicle membrane / glutamate secretion / cellular response to interleukin-7 / myosin binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / brush border / endocytic vesicle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein targeting / endothelial cell migration / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / dendritic shaft / PDZ domain binding / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / regulation of protein stability / synaptic vesicle / presynapse / actin binding / cell cortex / chemical synaptic transmission / cytoplasmic vesicle / postsynapse / dendritic spine / G protein-coupled receptor signaling pathway / signaling receptor binding / glutamatergic synapse / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
PDZ domain-containing protein GIPC1/2/3 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
PDZ domain-containing protein GIPC1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsBarthe, P. / Roumestand, C.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Pressure and Chemical Unfolding of an alpha-Helical Bundle Protein: The GH2 Domain of the Protein Adaptor GIPC1.
Authors: Dubois, C. / Planelles-Herrero, V.J. / Tillatte-Tripodi, C. / Delbecq, S. / Mammri, L. / Sirkia, E.M. / Ropars, V. / Roumestand, C. / Barthe, P.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDZ domain-containing protein GIPC1


Theoretical massNumber of molelcules
Total (without water)9,1811
Polymers9,1811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PDZ domain-containing protein GIPC1 / GAIP C-terminus-interacting protein / RGS-GAIP-interacting protein / RGS19-interacting protein 1 / ...GAIP C-terminus-interacting protein / RGS-GAIP-interacting protein / RGS19-interacting protein 1 / SemaF cytoplasmic domain-associated protein 1 / SEMCAP-1 / Synectin


Mass: 9181.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gipc1, Gipc, Rgs19ip1, Semcap1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z0G0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic13D HN(CA)CB
132isotropic13D HNCO
143isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-15N] GIPC1-GH2, 20 mM TRIS, 0.1 mM EDTA, 0.1 mM PMSF, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution21.0 mM [U-13C; U-15N] GIPC1-GH2, 20 mM TRIS, 0.1 mM EDTA, 0.1 mM PMSF, 95% H2O/5% D2O13C_sample95% H2O/5% D2O
solution31.0 mM GIPC1-GH2, 20 mM TRIS, 0.1 mM EDTA, 0.1 mM PMSF, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMGIPC1-GH2[U-15N]1
20 mMTRISnatural abundance1
0.1 mMEDTAnatural abundance1
0.1 mMPMSFnatural abundance1
1.0 mMGIPC1-GH2[U-13C; U-15N]2
20 mMTRISnatural abundance2
0.1 mMEDTAnatural abundance2
0.1 mMPMSFnatural abundance2
1.0 mMGIPC1-GH2natural abundance3
20 mMTRISnatural abundance3
0.1 mMEDTAnatural abundance3
0.1 mMPMSFnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CINDYPadillachemical shift assignment
CINDYPadillapeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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