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- PDB-2es0: Structure of the regulator of G-protein signaling domain of RGS6 -

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Basic information

Entry
Database: PDB / ID: 2es0
TitleStructure of the regulator of G-protein signaling domain of RGS6
Componentsregulator of G-protein signalling 6
KeywordsSIGNALING PROTEIN / HUMAN RGS6 / REGULATOR OF G-PROTEIN SIGNALING 6 / GTPASE-ACTIVATING PROTEINS (GAP) / DOMAIN SWAP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / extrinsic component of membrane / negative regulation of signal transduction / GTPase activator activity / positive regulation of GTPase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G alpha (i) signalling events / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity ...regulation of G protein-coupled receptor signaling pathway / extrinsic component of membrane / negative regulation of signal transduction / GTPase activator activity / positive regulation of GTPase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G alpha (i) signalling events / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / nucleus / plasma membrane / cytosol
Similarity search - Function
RGS6, RGS domain / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain ...RGS6, RGS domain / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchoch, G.A. / Phillips, C. / Turnbull, A. / Niesen, F. / Johansson, C. / Elkins, J.M. / Longman, E. / Gilealdi, C. / Sobott, F. / Ball, L. ...Schoch, G.A. / Phillips, C. / Turnbull, A. / Niesen, F. / Johansson, C. / Elkins, J.M. / Longman, E. / Gilealdi, C. / Sobott, F. / Ball, L. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / 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
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 signalling 6


Theoretical massNumber of molelcules
Total (without water)17,2371
Polymers17,2371
Non-polymers00
Water2,414134
1
A: regulator of G-protein signalling 6

A: regulator of G-protein signalling 6


Theoretical massNumber of molelcules
Total (without water)34,4732
Polymers34,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6320 Å2
ΔGint-50 kcal/mol
Surface area14350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.567, 77.567, 73.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

DetailsDimer, with domain swap Form a biological unit with symmetry related molecule (X, Y, -Z)

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Components

#1: Protein regulator of G-protein signalling 6


Mass: 17236.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pLIC-SGC / Production host: Escherichia coli (E. coli) / References: UniProt: P49758
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 10K; (NH4)(ac); BIS-TRIS , pH pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→72.93 Å / Num. all: 15210 / Num. obs: 15210 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 43.143 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.089 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.01088 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2183 / Rsym value: 0.01204 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A72.pdb

2a72


Resolution: 2.1→67.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.654 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22855 763 5 %RANDOM
Rwork0.19474 ---
obs0.19636 14413 99.86 %-
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: 43.143 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å21.13 Å20 Å2
2--2.25 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 134 1195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221101
X-RAY DIFFRACTIONr_bond_other_d0.0010.02965
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9421487
X-RAY DIFFRACTIONr_angle_other_deg0.74432247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5824.26261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69115195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.378158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
X-RAY DIFFRACTIONr_nbd_refined0.2020.2267
X-RAY DIFFRACTIONr_nbd_other0.1650.2896
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2554
X-RAY DIFFRACTIONr_nbtor_other0.0820.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4511.5673
X-RAY DIFFRACTIONr_mcbond_other0.0841.5263
X-RAY DIFFRACTIONr_mcangle_it0.7521043
X-RAY DIFFRACTIONr_scbond_it1.1063498
X-RAY DIFFRACTIONr_scangle_it1.84.5442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 51 -
Rwork0.32 1045 -
obs--99.1 %
Refinement TLS params.Method: refined / Origin x: 13.3 Å / Origin y: 35.5591 Å / Origin z: 2.5897 Å
111213212223313233
T-0.1546 Å2-0.0511 Å2-0.0541 Å2--0.182 Å20.0497 Å2---0.1974 Å2
L5.1292 °2-2.9337 °2-2.6095 °2-2.5416 °21.61 °2--2.1981 °2
S-0.1103 Å °-0.0351 Å °0.0396 Å °0.1714 Å °0.2059 Å °0.0118 Å °0.2014 Å °-0.0734 Å °-0.0956 Å °

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