[English] 日本語
Yorodumi
- PDB-4ekc: Structure of human regulator of G protein signaling 2 (RGS2) in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ekc
TitleStructure of human regulator of G protein signaling 2 (RGS2) in complex with murine Galpha-q(R183C)
Components
  • Guanine nucleotide-binding protein G(q) subunit alpha
  • Regulator of G-protein signaling 2
KeywordsSIGNALING PROTEIN/INHIBITOR / GTP-binding protein fold / Regulator / G protein signaling / RGS / homology domain / GTPase activation / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / 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 / adenylate cyclase inhibitor activity / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding ...regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / 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 / adenylate cyclase inhibitor activity / forebrain neuron development / regulation of melanocyte differentiation / 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 / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of G protein-coupled receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / regulation of platelet activation / ADP signalling through P2Y purinoceptor 1 / maternal behavior / regulation of G protein-coupled receptor signaling pathway / relaxation of vascular associated smooth muscle / glutamate receptor signaling pathway / regulation of canonical Wnt signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / relaxation of cardiac muscle / action potential / neuron remodeling / embryonic digit morphogenesis / beta-tubulin binding / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / G-protein alpha-subunit binding / maternal process involved in female pregnancy / enzyme regulator activity / brown fat cell differentiation / positive regulation of cardiac muscle contraction / response to amphetamine / GTPase activator activity / post-embryonic development / negative regulation of MAP kinase activity / G protein activity / skeletal system development / G protein-coupled receptor binding / caveola / positive regulation of smooth muscle cell proliferation / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / positive regulation of insulin secretion / regulation of blood pressure / heterotrimeric G-protein complex / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / G alpha (q) signalling events / spermatogenesis / response to ethanol / nuclear membrane / negative regulation of translation / protein stabilization / calmodulin binding / cell cycle / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / protein-containing complex binding / GTP binding / nucleolus / negative regulation of apoptotic process / Golgi apparatus / mitochondrion / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 2 / RGS, subdomain 1/3 / G-protein alpha subunit, group Q / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / G-alpha domain profile. ...Regulator of G-protein signalling 2 / RGS, subdomain 1/3 / G-protein alpha subunit, group Q / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(q) subunit alpha / Regulator of G-protein signaling 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.4 Å
AuthorsTesmer, J.J.G. / Nance, M.R.
CitationJournal: 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.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(q) subunit alpha
B: Regulator of G-protein signaling 2
C: Guanine nucleotide-binding protein G(q) subunit alpha
D: Regulator of G-protein signaling 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,15310
Polymers113,0124
Non-polymers1,1416
Water1086
1
A: Guanine nucleotide-binding protein G(q) subunit alpha
B: Regulator of G-protein signaling 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0765
Polymers56,5062
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Guanine nucleotide-binding protein G(q) subunit alpha
D: Regulator of G-protein signaling 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0765
Polymers56,5062
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.603, 124.983, 97.196
Angle α, β, γ (deg.)90.00, 124.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.705688, 0.002919, 0.708516), (-0.009257, -0.999944, -0.005101), (0.708462, -0.010158, 0.705676)21.99455, 14.7859, -9.2763

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein alpha-q


Mass: 40634.172 Da / Num. of mol.: 2 / 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: 3.6.5.1
#2: Protein Regulator of G-protein signaling 2 / RGS2 / Cell growth-inhibiting gene 31 protein / G0/G1 switch regulatory protein 8


Mass: 15871.833 Da / Num. of mol.: 2 / 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 , 4 types, 12 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 3350, 200 mM NaCl, and 100 mM MES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 18, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 7.4→30 Å / Num. all: 1841 / Num. obs: 1820 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Rsym value: 0.156 / Net I/σ(I): 9.1
Reflection shellResolution: 7.4→7.53 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 78 / Rsym value: 0.518 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2AF0 and 2BCJ

2af0

2bcj


Resolution: 7.4→19.98 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.907 / SU B: 397.868 / SU ML: 3.017 / Cross valid method: THROUGHOUT / ESU R Free: 3.543 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22037 76 4.3 %RANDOM
Rwork0.15796 ---
all0.16084 1690 --
obs0.16084 1690 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 121.291 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 7.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7318 0 68 6 7392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027544
X-RAY DIFFRACTIONr_bond_other_d0.0020.025202
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.96810198
X-RAY DIFFRACTIONr_angle_other_deg0.932312636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53424.323384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.446151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6351548
X-RAY DIFFRACTIONr_chiral_restr0.0480.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.4→7.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.271 89 -
Rfree-0 -
obs--88.12 %

+
About Yorodumi

-
News

-
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

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

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

Read more