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- PDB-2jx0: The paxillin-binding domain (PBD) of G Protein Coupled Receptor (... -

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Basic information

Entry
Database: PDB / ID: 2jx0
TitleThe paxillin-binding domain (PBD) of G Protein Coupled Receptor (GPCR)-kinase (GRK) interacting protein 1 (GIT1)
ComponentsARF GTPase-activating protein GIT1
KeywordsCELL ADHESION / SIGNALING PROTEIN / paxillin binding domain homologue / ANK repeat / Cytoplasm / GTPase activation / Metal-binding / Phosphorylation / Zinc / Zinc-finger
Function / homology
Function and homology information


negative regulation of ARF protein signal transduction / structural constituent of postsynaptic specialization / Ephrin signaling / RAC2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / motor learning / synaptic vesicle recycling ...negative regulation of ARF protein signal transduction / structural constituent of postsynaptic specialization / Ephrin signaling / RAC2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / motor learning / synaptic vesicle recycling / negative regulation of inflammatory response to wounding / intramembranous ossification / inhibitory synapse / immunological synapse formation / positive regulation of microtubule nucleation / regulation of ARF protein signal transduction / dendritic spine development / regulation of G protein-coupled receptor signaling pathway / gamma-tubulin binding / negative regulation of glycolytic process / negative regulation of interleukin-1 beta production / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synaptic vesicle exocytosis / positive regulation of receptor catabolic process / mitotic spindle pole / excitatory synapse / calyx of Held / ephrin receptor signaling pathway / neuron development / GABA-ergic synapse / cellular response to epidermal growth factor stimulus / presynaptic modulation of chemical synaptic transmission / protein tyrosine kinase binding / GTPase activator activity / cell redox homeostasis / regulation of cytokinesis / locomotory behavior / brain development / small GTPase binding / lamellipodium / presynapse / growth cone / scaffold protein binding / cellular response to lipopolysaccharide / protein phosphatase binding / postsynapse / postsynaptic density / endosome / neuron projection / focal adhesion / centrosome / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Arf GTPase-activating protein GIT1/2, coiled-coil domain / GIT coiled-coil Rho guanine nucleotide exchange factor / : / GIT, Spa2 homology (SHD) domain / ARF GTPase-activating protein GIT1, C-terminal / Spa2 homology domain (SHD) of GIT / G protein-coupled receptor kinase-interacting protein 1 C term / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / Arf GTPase activating protein / ArfGAP domain superfamily ...Arf GTPase-activating protein GIT1/2, coiled-coil domain / GIT coiled-coil Rho guanine nucleotide exchange factor / : / GIT, Spa2 homology (SHD) domain / ARF GTPase-activating protein GIT1, C-terminal / Spa2 homology domain (SHD) of GIT / G protein-coupled receptor kinase-interacting protein 1 C term / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / Nucleotidyltransferases domain 2 / ARFGAP/RecO-like zinc finger / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ARF GTPase-activating protein GIT1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhang, Z. / Guibao, C.D. / Simmerman, J.A. / Zheng, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: GIT1 paxillin-binding domain is a four-helix bundle, and it binds to both paxillin LD2 and LD4 motifs.
Authors: Zhang, Z.M. / Simmerman, J.A. / Guibao, C.D. / Zheng, J.J.
History
DepositionNov 1, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: ARF GTPase-activating protein GIT1


Theoretical massNumber of molelcules
Total (without water)15,0291
Polymers15,0291
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein ARF GTPase-activating protein GIT1 / G protein-coupled receptor kinase-interactor 1 / GRK-interacting protein 1 / Cool-associated and ...G protein-coupled receptor kinase-interactor 1 / GRK-interacting protein 1 / Cool-associated and tyrosine-phosphorylated protein 1 / Cat-1


Mass: 15029.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Git1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z272

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D (H)CCH-COSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-99% 15N] GT, 20 mM potassium phosphate, 5 mM DTT, 5 mM EDTA, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMGT[U-99% 13C; U-99% 15N]1
20 mMpotassium phosphate1
5 mMDTT1
5 mMEDTA1
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CYANA / Version: 2 / Developer: GUNTERT, P. ET AL. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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