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- PDB-2ihd: Crystal structure of Human Regulator of G-protein signaling 8, RGS8 -

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Basic information

Entry
Database: PDB / ID: 2ihd
TitleCrystal structure of Human Regulator of G-protein signaling 8, RGS8
ComponentsRegulator of G-protein signaling 8
KeywordsSIGNALING PROTEIN / RGS8 / RGS / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of dopamine receptor signaling pathway / neuronal cell body membrane / negative regulation of signal transduction / GTPase activator activity / positive regulation of GTPase activity / G protein-coupled acetylcholine receptor signaling pathway / cytoplasmic side of plasma membrane / G alpha (i) signalling events / perikaryon / G protein-coupled receptor signaling pathway ...regulation of dopamine receptor signaling pathway / neuronal cell body membrane / negative regulation of signal transduction / GTPase activator activity / positive regulation of GTPase activity / G protein-coupled acetylcholine receptor signaling pathway / cytoplasmic side of plasma membrane / G alpha (i) signalling events / perikaryon / G protein-coupled receptor signaling pathway / GTPase activity / synapse / dendrite / nucleus / plasma membrane
Similarity search - Function
Regulator of G-protein signalling 8, RGS domain / 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, subdomain 2 / RGS domain / RGS domain profile. ...Regulator of G-protein signalling 8, RGS domain / 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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTurnbull, A.P. / Papagrigoriou, E. / Ugochukwu, E. / Salah, E. / Gileadi, C. / Burgess, N. / Bhatia, C. / Gileadi, O. / Bray, J. / Elkins, J. ...Turnbull, A.P. / Papagrigoriou, E. / Ugochukwu, E. / Salah, E. / Gileadi, C. / Burgess, N. / Bhatia, C. / Gileadi, O. / Bray, J. / Elkins, J. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / 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
DepositionSep 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2682
Polymers18,2331
Non-polymers351
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.967, 65.967, 76.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

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Components

#1: Protein Regulator of G-protein signaling 8 / RGS8


Mass: 18232.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS8 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta / References: UniProt: P57771
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20M NaI; 20.0% PEG 3350; 10.0% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 16, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 17206 / Num. obs: 17199 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel based on pdb entry 2BT2

2bt2


Resolution: 1.7→27.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.803 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21119 878 5.1 %RANDOM
Rwork0.17524 ---
all0.17707 16320 --
obs0.17707 16320 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 1 170 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221090
X-RAY DIFFRACTIONr_bond_other_d0.0010.02777
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9441472
X-RAY DIFFRACTIONr_angle_other_deg0.90131877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7395134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11523.03656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28315201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0251510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.2130.2266
X-RAY DIFFRACTIONr_nbd_other0.1750.2815
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2550
X-RAY DIFFRACTIONr_nbtor_other0.0820.2517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
X-RAY DIFFRACTIONr_mcbond_it3.0245647
X-RAY DIFFRACTIONr_mcbond_other1.1925256
X-RAY DIFFRACTIONr_mcangle_it4.13571046
X-RAY DIFFRACTIONr_scbond_it6.3849456
X-RAY DIFFRACTIONr_scangle_it8.63212422
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 60 -
Rwork0.243 1256 -
obs--99.62 %
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)
14.76850.8619-0.14934.4938-1.75682.67850.06810.19230.8379-0.0818-0.0006-0.0752-0.5561-0.0687-0.06760.1933-0.0280.01470.05130.02030.177423.1119-4.02562.0716
22.51220.46542.61090.77631.43884.8464-0.05680.07410.0283-0.1410.10860.10260.0636-0.1027-0.05180.0753-0.024-0.01710.05350.00360.045923.1978-16.65177.4898
31.6910.61750.89961.79571.86225.7165-0.0565-0.21320.02040.13550.07810.035-0.02320.1613-0.02160.0760.0351-0.00980.1292-0.01560.08829.4288-14.690523.2787
44.93313.90490.22553.5058-1.14864.2559-0.3076-0.0344-0.5031-0.3470.1608-0.48460.52390.11420.14680.1650.03530.03050.049-0.01990.148628.2783-25.698412.8515
52.3252-0.056-0.3542.5674-0.25873.7784-0.1549-0.1248-0.03660.0450.0931-0.28530.45570.44030.06190.12960.05230.01950.1458-0.02850.10237.1318-19.203515.9492
612.3591-5.39112.86756.048-0.890510.89820.35840.8460.3025-0.7821-0.42220.2243-0.4671-0.06750.06380.08080.0008-0.01-0.03040.0289-0.054723.1219-9.7982-4.9392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA46 - 7428 - 56
2X-RAY DIFFRACTION2AA75 - 8757 - 69
3X-RAY DIFFRACTION3AA88 - 11470 - 96
4X-RAY DIFFRACTION4AA115 - 12497 - 106
5X-RAY DIFFRACTION5AA125 - 154107 - 136
6X-RAY DIFFRACTION6AA155 - 172137 - 154

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