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

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Basic information

Entry
Database: PDB / ID: 4ekd
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 / Regulator of G protein signaling / 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 / beta-tubulin binding / brown fat cell differentiation / 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 / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / G-protein alpha subunit, group Q / 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 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / G-protein alpha subunit, group Q / 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 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 2.71 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 1.2Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,46010
Polymers56,5062
Non-polymers9548
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.248, 60.248, 345.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

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


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: 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.: 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

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Non-polymers , 7 types, 24 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2010 / Details: KB Bimorph Mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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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: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 572 4.9 %RANDOM
Rwork0.1901 ---
all0.19298 11078 --
obs0.19298 11078 63.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.352 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 50 16 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023823
X-RAY DIFFRACTIONr_bond_other_d0.0010.022647
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9715167
X-RAY DIFFRACTIONr_angle_other_deg0.80136431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87524.301193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08615686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8091524
X-RAY DIFFRACTIONr_chiral_restr0.0560.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
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: 2.71→2.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 9 -
Rwork0.333 199 -
obs--16.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08560.2225-0.2170.6792-0.38223.12960.0172-0.02170.02-0.0445-0.1226-0.0860.29620.13990.10530.67870.04680.10410.7683-0.0670.3489-27.34818.003-22.185
21.28181.15911.02073.898-0.08061.29590.11130.09880.10610.07330.03420.1630.1912-0.0209-0.14550.6362-0.10950.09780.90960.05250.3827-52.43721.203-23.362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 354
2X-RAY DIFFRACTION1A401 - 407
3X-RAY DIFFRACTION1A501 - 503
4X-RAY DIFFRACTION1A504 - 515
5X-RAY DIFFRACTION2B69 - 200
6X-RAY DIFFRACTION2B301
7X-RAY DIFFRACTION2B401

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