|Entry||Database: PDB / ID: 4ekd|
|Title||Structure of human regulator of G protein signaling 2 (RGS2) in complex with murine Galpha-q(R183C)|
|Keywords||SIGNALING PROTEIN/INHIBITOR / GTP-binding / Regulator of G protein signaling / homology domain / GTPase activation / SIGNALING PROTEIN-INHIBITOR complex|
|Function / homology|
Function and homology information
negative regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / adenylate cyclase inhibitor activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding ...negative regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / adenylate cyclase inhibitor activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / G alpha (q) signalling events / endothelin receptor signaling pathway / developmental pigmentation / phospholipase C-activating dopamine receptor signaling pathway / ovulation / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / cranial skeletal system development / regulation of platelet activation / regulation of G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / glutamate receptor signaling pathway / maternal behavior / multicellular organism aging / alkylglycerophosphoethanolamine phosphodiesterase activity / regulation of canonical Wnt signaling pathway / relaxation of vascular associated smooth muscle / action potential / beta-tubulin binding / relaxation of cardiac muscle / embryonic digit morphogenesis / brown fat cell differentiation / neuron remodeling / G-protein alpha-subunit binding / activation of phospholipase C activity / negative regulation of potassium ion transport / maternal process involved in female pregnancy / cytoplasmic side of plasma membrane / positive regulation of cardiac muscle contraction / G-protein beta/gamma-subunit complex binding / response to amphetamine / post-embryonic development / GTPase activator activity / heterotrimeric G-protein complex / positive regulation of smooth muscle cell proliferation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / skeletal system development / positive regulation of neuron projection development / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of MAP kinase activity / caveola / phospholipase C-activating G protein-coupled receptor signaling pathway / G protein-coupled receptor binding / negative regulation of protein kinase activity / regulation of blood pressure / cell body / G alpha (q) signalling events / brain development / spermatogenesis / heart development / negative regulation of translation / nuclear membrane / response to ethanol / calmodulin binding / protein stabilization / G protein-coupled receptor signaling pathway / cell cycle / GTPase activity / neuron projection / synapse / dendrite / protein-containing complex binding / GTP binding / nucleolus / negative regulation of apoptotic process / Golgi apparatus / mitochondrion / membrane / metal ion binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 2 / Regulator of G-protein Signalling 4; domain 1 - #10 / G-protein alpha subunit, group Q / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain ...Regulator of G-protein signalling 2 / Regulator of G-protein Signalling 4; domain 1 - #10 / G-protein alpha subunit, group Q / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain profile. / Regulator of G protein signalling domain / RGS domain / RGS domain superfamily / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G protein alpha subunit, helical insertion / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(q) subunit alpha / TETRAFLUOROALUMINATE ION / : / GUANOSINE-5'-DIPHOSPHATE / Regulator of G-protein signaling 2
Similarity search - Component
|Biological species||Mus musculus (house mouse)|
Homo sapiens (human)
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å|
|Authors||Tesmer, J.J.G. / Nance, M.R.|
|Citation||Journal: Structure / Year: 2013|
Title: Structural and functional analysis of the regulator of G protein signaling 2-g alpha q complex.
Authors: Nance, M.R. / Kreutz, B. / Tesmer, V.M. / Sterne-Marr, R. / Kozasa, T. / Tesmer, J.J.
|Structure viewer||Molecule: |
Downloads & links
A: Guanine nucleotide-binding protein G(q) subunit alpha
B: Regulator of G-protein signaling 2
-Protein , 2 types, 2 molecules A
|#1: Protein|| |
Mass: 40634.172 Da / Num. of mol.: 1 / Fragment: UNP residues 18-359 / Mutation: E125D, N126V, Y128D, V129Y, D130A, R183C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21279, EC: 188.8.131.52
|#2: Protein|| |
Mass: 15871.833 Da / Num. of mol.: 1 / Fragment: RGS domain, UNP residues 72-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS2, G0S8, GIG31 / Production host: Escherichia coli (E. coli) / References: UniProt: P41220
-Non-polymers , 7 types, 24 molecules
|#3: Chemical|| ChemComp-GDP / |
|#4: Chemical|| ChemComp-ALF / |
|#5: Chemical||#6: Chemical||#7: Chemical|| ChemComp-MG / ||#8: Chemical|| ChemComp-MES / ||#9: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 %|
|Crystal grow||Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 |
Details: 12% PEG 8,000, 15 mM CoCl2, 200 mM NaCl, and 100 mM MES 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|Diffraction||Mean temperature: 110 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å|
|Detector||Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2010 / Details: KB Bimorph Mirrors|
|Radiation||Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.0782 Å / Relative weight: 1|
|Reflection||Resolution: 2.7→30 Å / Num. all: 12037 / Num. obs: 11782 / % possible obs: 64 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.065 / Net I/σ(I): 24.9|
|Reflection shell||Resolution: 2.7→2.75 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 189 / Rsym value: 0.441 / % possible all: 21.4|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: PDB entries 2AF0 and 2BCJ
Resolution: 2.71→29.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 44.27 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK|
|Displacement parameters||Biso mean: 96.352 Å2|
|Refinement step||Cycle: LAST / Resolution: 2.71→29.98 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2.71→2.782 Å / Total num. of bins used: 20 |
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
-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