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- PDB-2af0: Structure of the Regulator of G-Protein Signaling Domain of RGS2 -

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Basic information

Entry
Database: PDB / ID: 2af0
TitleStructure of the Regulator of G-Protein Signaling Domain of RGS2
ComponentsRegulator of G-protein signaling 2
KeywordsSIGNALING PROTEIN / HELIX / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of glycine import across plasma membrane / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / relaxation of vascular associated smooth muscle / regulation of G protein-coupled receptor signaling pathway / relaxation of cardiac muscle / negative regulation of JNK cascade / negative regulation of G protein-coupled receptor signaling pathway / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway ...regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of glycine import across plasma membrane / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / relaxation of vascular associated smooth muscle / regulation of G protein-coupled receptor signaling pathway / relaxation of cardiac muscle / negative regulation of JNK cascade / negative regulation of G protein-coupled receptor signaling pathway / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / G-protein alpha-subunit binding / maternal process involved in female pregnancy / beta-tubulin binding / brown fat cell differentiation / adenylate cyclase inhibitor activity / positive regulation of cardiac muscle contraction / GTPase activator activity / response to amphetamine / positive regulation of neuron projection development / cytoplasmic side of plasma membrane / response to ethanol / spermatogenesis / G alpha (q) signalling events / calmodulin binding / negative regulation of translation / G protein-coupled receptor signaling pathway / GTPase activity / nucleolus / mitochondrion / nucleus / plasma membrane / cytosol / cytoplasm
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 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling 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 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPapagrigoriou, E. / Johannson, C. / Phillips, C. / Smee, C. / Elkins, J.M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Von Delft, F. ...Papagrigoriou, E. / Johannson, C. / Phillips, C. / Smee, C. / Elkins, J.M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Von Delft, F. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural diversity in the RGS domain and its interaction with heterotrimeric G protein alpha-subunits.
Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / ...Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / Doyle, D.A. / Siderovski, D.P.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of G-protein signaling 2


Theoretical massNumber of molelcules
Total (without water)16,9941
Polymers16,9941
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.754, 43.754, 158.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Regulator of G-protein signaling 2 / RGS2 / G0/G1 switch regulatory protein 8


Mass: 16994.148 Da / Num. of mol.: 1 / Fragment: residues 71-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P41220
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4, NaCl, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9773 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9773 Å / Relative weight: 1
ReflectionResolution: 2.3→36.9 Å / Num. all: 7531 / Num. obs: 7422 / % possible obs: 98.6 %
Reflection shellResolution: 2.3→2.38 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.946 / SU B: 22.428 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 345 4.8 %RANDOM
Rwork0.22575 ---
all0.2721 ---
obs0.22721 6833 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.407 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2--3.24 Å20 Å2
3----6.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 0 17 1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221176
X-RAY DIFFRACTIONr_bond_other_d0.0010.021008
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9521592
X-RAY DIFFRACTIONr_angle_other_deg0.82932349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30625.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83215191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.876154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02249
X-RAY DIFFRACTIONr_nbd_refined0.2170.2274
X-RAY DIFFRACTIONr_nbd_other0.1740.2937
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2594
X-RAY DIFFRACTIONr_nbtor_other0.0870.2590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5331.5755
X-RAY DIFFRACTIONr_mcbond_other0.1051.5291
X-RAY DIFFRACTIONr_mcangle_it0.93721169
X-RAY DIFFRACTIONr_scbond_it1.3313489
X-RAY DIFFRACTIONr_scangle_it2.1034.5423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 31 -
Rwork0.294 478 -
obs--100 %

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