|Entry||Database: PDB / ID: 2jx0|
|Title||The paxillin-binding domain (PBD) of G Protein Coupled Receptor (GPCR)-kinase (GRK) interacting protein 1 (GIT1)|
|Components||ARF GTPase-activating protein GIT1|
|Keywords||CELL 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 / negative regulation of inflammatory response to wounding / structural constituent of postsynaptic specialization / RAC3 GTPase cycle / Ephrin signaling / RAC2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / motor learning / RHOJ GTPase cycle ...negative regulation of ARF protein signal transduction / negative regulation of inflammatory response to wounding / structural constituent of postsynaptic specialization / RAC3 GTPase cycle / Ephrin signaling / RAC2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / motor learning / RHOJ GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / CDC42 GTPase cycle / synaptic vesicle recycling / regulation of ARF protein signal transduction / presynaptic modulation of chemical synaptic transmission / immunological synapse formation / intramembranous ossification / positive regulation of microtubule nucleation / dendritic spine development / regulation of G protein-coupled receptor signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / gamma-tubulin binding / negative regulation of glycolytic process / negative regulation of interleukin-1 beta production / positive regulation of receptor catabolic process / mitotic spindle pole / neuron development / GABA-ergic synapse / calyx of Held / ephrin receptor signaling pathway / cellular response to epidermal growth factor stimulus / GTPase activator activity / locomotory behavior / cell redox homeostasis / regulation of cytokinesis / regulation of synaptic vesicle exocytosis / small GTPase binding / postsynapse / lamellipodium / brain development / postsynaptic density / endosome / cellular response to lipopolysaccharide / centrosome / neuron projection / glutamatergic synapse / synapse / focal adhesion / protein-containing complex binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
GIT coiled-coil Rho guanine nucleotide exchange factor / Arf GTPase-activating protein GIT1/2, coiled-coil domain / ARF GTPase-activating protein GIT1, C-terminal / G protein-coupled receptor kinase-interacting protein 1 C term / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / GIT, Spa2 homology (SHD) domain / Spa2 homology domain (SHD) of GIT / Putative GTPase activating protein for Arf / ArfGAP domain superfamily / Arf GTPase activating protein ...GIT coiled-coil Rho guanine nucleotide exchange factor / Arf GTPase-activating protein GIT1/2, coiled-coil domain / ARF GTPase-activating protein GIT1, C-terminal / G protein-coupled receptor kinase-interacting protein 1 C term / Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins / GIT, Spa2 homology (SHD) domain / Spa2 homology domain (SHD) of GIT / Putative GTPase activating protein for Arf / ArfGAP domain superfamily / Arf GTPase activating protein / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / Ankyrin repeat 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 species||Rattus norvegicus (Norway rat)|
|Method||SOLUTION NMR / torsion angle dynamics|
|Authors||Zhang, Z. / Guibao, C.D. / Simmerman, J.A. / Zheng, J.|
|Citation||Journal: 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.
|Structure viewer||Molecule: |
Downloads & links
A: ARF GTPase-activating protein GIT1
|#1: Protein|| |
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) (unknown) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z272
|Experiment||Method: SOLUTION NMR|
|Details||Contents: 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 conditions||Ionic strength: 20 / pH: 6.50 / Pressure: AMBIENT / Temperature: 310 K|
|NMR software||Name: CYANA / Version: 2 / Developer: GUNTERT, P. ET AL. / Classification: refinement|
|Refinement||Method: torsion angle dynamics / Software ordinal: 1|
|NMR representative||Selection criteria: closest to the average|
|NMR ensemble||Conformer selection criteria: structures with the least restraint violations|
Conformers calculated total number: 100 / Conformers submitted total number: 20
-Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
- Version 3 of the EMDB header file is now the official format.
- The previous official version 1.9 will be removed from the archive.
Related info.:EMDB header
External links:wwPDB to switch to version 3 of the EMDB data model
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi