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- PDB-4ekc: Structure of human regulator of G protein signaling 2 (RGS2) in c... -

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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 glycine import across plasma membrane / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / PLC beta mediated events / Acetylcholine regulates insulin secretion / 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) ...regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of glycine import across plasma membrane / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / PLC beta mediated events / Acetylcholine regulates insulin secretion / 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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G alpha (q) signalling events / endothelin receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / developmental pigmentation / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / ADP signalling through P2Y purinoceptor 1 / regulation of platelet activation / cranial skeletal system development / relaxation of vascular associated smooth muscle / regulation of G protein-coupled receptor signaling pathway / maternal behavior / relaxation of cardiac muscle / negative regulation of JNK cascade / negative regulation of G protein-coupled receptor signaling pathway / embryonic digit morphogenesis / glutamate receptor signaling pathway / neuron remodeling / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / ligand-gated ion channel signaling pathway / action potential / G-protein alpha-subunit binding / maternal process involved in female pregnancy / postsynaptic cytosol / brown fat cell differentiation / beta-tubulin binding / adenylate cyclase inhibitor activity / enzyme regulator activity / positive regulation of cardiac muscle contraction / GTPase activator activity / response to amphetamine / post-embryonic development / skeletal system development / G protein-coupled receptor binding / positive regulation of neuron projection development / positive regulation of insulin secretion / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / cytoplasmic side of plasma membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / heart development / G protein activity / cell body / response to ethanol / spermatogenesis / nuclear membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / calmodulin binding / negative regulation of translation / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / GTP binding / nucleolus / Golgi apparatus / mitochondrion / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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 domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Guanine nucleotide binding protein (G-protein), alpha subunit ...Regulator of G-protein signalling 2 / RGS, subdomain 1/3 / G-protein alpha subunit, group Q / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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Non-polymers , 4 types, 12 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-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


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

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Experimental details

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Experiment

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

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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

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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

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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 %

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