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- PDB-2gtp: Crystal structure of the heterodimeric complex of human RGS1 and ... -

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Basic information

Entry
Database: PDB / ID: 2gtp
TitleCrystal structure of the heterodimeric complex of human RGS1 and activated Gi alpha 1
Components
  • Guanine nucleotide-binding protein G(i), alpha-1 subunit
  • Regulator of G-protein signaling 1
KeywordsSIGNALING PROTEIN / G protein signalling / RGS / heterotrimeric G protein / signalling complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


leukotriene signaling pathway / regulation of G protein-coupled receptor signaling pathway / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / cell cortex region / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / G-protein alpha-subunit binding / regulation of mitotic spindle organization / cellular response to forskolin ...leukotriene signaling pathway / regulation of G protein-coupled receptor signaling pathway / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / cell cortex region / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / G-protein alpha-subunit binding / regulation of mitotic spindle organization / cellular response to forskolin / negative regulation of signal transduction / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G alpha (z) signalling events / GTPase activator activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GPER1 signaling / heterotrimeric G-protein complex / response to bacterium / response to peptide hormone / ADORA2B mediated anti-inflammatory cytokines production / extrinsic component of cytoplasmic side of plasma membrane / G protein-coupled receptor binding / GDP binding / G alpha (i) signalling events / positive regulation of GTPase activity / G alpha (s) signalling events / cell cortex / G alpha (q) signalling events / midbody / Extra-nuclear estrogen signaling / calmodulin binding / lysosomal membrane / G protein-coupled receptor signaling pathway / immune response / cell cycle / cell division / centrosome / GTPase activity / GTP binding / magnesium ion binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 1 / 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 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 ...Regulator of G-protein signalling 1 / 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 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Regulator of G-protein signaling 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSoundararajan, M. / Turnbull, A.P. / Ugochukwu, E. / Gorrec, F. / 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
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
B: Guanine nucleotide-binding protein G(i), alpha-1 subunit
C: Regulator of G-protein signaling 1
D: Regulator of G-protein signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,35510
Polymers107,2144
Non-polymers1,1416
Water2,414134
1
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
D: Regulator of G-protein signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1775
Polymers53,6072
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanine nucleotide-binding protein G(i), alpha-1 subunit
C: Regulator of G-protein signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1775
Polymers53,6072
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.451, 102.904, 128.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGLEUAA32 - 3481 - 317
21ARGLEUBB32 - 3481 - 317
12TRPGLNCC69 - 19122 - 144
22TRPGLNDD69 - 19122 - 144

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Guanine nucleotide-binding protein G(i), alpha-1 subunit / Adenylate cyclase-inhibiting G alpha protein


Mass: 37031.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P63096
#2: Protein Regulator of G-protein signaling 1 / RGS1 / Early response protein 1R20 / B-cell activation protein BL34


Mass: 16575.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: Q08116

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Non-polymers , 4 types, 140 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaNO3, 0.1M bis-Tris propane, pH 6.5, 20 % PEG3350, 10 % 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: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 39406 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.55→2.64 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDs 2BV1 and 1Y3A used as starting models for RGS1 and GNAI1 respectively.
Resolution: 2.55→46.7 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.661 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27562 1976 5 %RANDOM
Rwork0.2259 ---
all0.22839 37274 --
obs0.22839 37274 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.466 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.44 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 68 134 7209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227207
X-RAY DIFFRACTIONr_bond_other_d0.0030.024720
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9569772
X-RAY DIFFRACTIONr_angle_other_deg0.964311517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6065886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46924.809341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.847151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0671533
X-RAY DIFFRACTIONr_chiral_restr0.0750.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028028
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021491
X-RAY DIFFRACTIONr_nbd_refined0.2150.21614
X-RAY DIFFRACTIONr_nbd_other0.1860.24817
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23645
X-RAY DIFFRACTIONr_nbtor_other0.0880.23714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2215
X-RAY DIFFRACTIONr_metal_ion_refined0.2110.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.23
X-RAY DIFFRACTIONr_mcbond_it0.3911.54571
X-RAY DIFFRACTIONr_mcbond_other0.1051.51794
X-RAY DIFFRACTIONr_mcangle_it0.66327128
X-RAY DIFFRACTIONr_scbond_it1.16433052
X-RAY DIFFRACTIONr_scangle_it1.724.52644
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1842tight positional0.070.05
2C732tight positional0.030.05
1A2204medium positional0.490.5
2C846medium positional0.270.5
1A1842tight thermal0.170.5
2C732tight thermal0.150.5
1A2204medium thermal0.452
2C846medium thermal0.292
LS refinement shellResolution: 2.55→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 136 -
Rwork0.292 2741 -
obs--98.76 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.86650.9861-1.21231.11920.10295.1109-0.127-0.04930.12760.16230.14170.674-0.0094-0.4248-0.01470.1011-0.01690.03680.0618-0.05820.023811.00238.24128.737
22.75590.6187-0.0513.46382.30642.65060.1023-0.2095-0.14160.0985-0.12660.3060.2266-0.3260.02420.1983-0.18230.02410.18660.02010.04053.92711.02322.62
30.86881.10750.33992.58160.28161.3515-0.04280.11460.1004-0.12260.03930.0906-0.0484-0.14120.00340.1588-0.03650.03420.1058-0.0126-0.004818.01935.3823.393
41.96840.147-0.00453.0003-0.52962.24750.0244-0.0941-0.05450.3850.0228-0.13540.07380.0867-0.04720.1567-0.03490.0050.1139-0.0366-0.033124.9330.1934.489
52.4553-1.89630.66981.47-0.61481.91110.1368-0.03710.5164-0.0546-0.1761-0.1891-0.23260.05250.03930.1744-0.04290.00370.0572-0.00710.0729-39.00218.65657.829
63.6533-1.99021.55624.1758-0.1715.95060.1237-0.19490.32240.0335-0.19970.0181-0.516-0.41060.0760.09750.1119-0.01020.194-0.09670.0327-59.2222.5550.848
72.0639-0.54750.30880.8699-0.34121.2470.02-0.18560.3723-0.0059-0.0705-0.2483-0.07120.06650.05050.1635-0.0401-0.01380.07-0.03570.0497-34.49415.66258.553
83.41210.3882-0.1331.5881-0.14962.37350.0543-0.2643-0.25420.0427-0.0566-0.02680.22630.07220.00230.1696-0.06330.00540.07430.0169-0.0036-39.940.00264.666
97.68872.13662.05413.329-3.16085.6397-0.19670.89051.5-0.74830.4996-0.2796-0.5470.3861-0.3030.4995-0.03280.23210.23630.22160.4057-25.55727.84438.102
106.39920.62536.90062.31940.00289.6747-0.10561.24790.1321-0.599-0.1137-0.0201-0.19231.01680.21930.3930.11590.07050.38050.0921-0.0242-33.79212.41929.977
114.494-5.4379-2.8018.52520.28556.69770.26550.749-0.11-0.3767-0.43590.32740.1877-0.14610.17040.12570.07970.00780.1817-0.0091-0.0726-38.7055.28837.757
125.1053.51262.50888.10262.3715.5453-0.06480.15510.5646-0.3253-0.2638-0.0246-0.5268-0.12820.32860.20110.10510.11180.07860.13620.0524-33.96919.3439.256
131.8552.06033.76065.22772.36348.7425-0.02420.31750.6113-0.91610.29451.638-0.211-1.9722-0.27030.34270.032-0.37280.70930.11940.5663-6.93937.0715.194
144.4547-0.94120.48276.60275.213910.28560.07180.5731-0.091-1.1534-0.05820.38750.2271-0.5111-0.01360.6902-0.1671-0.07390.17480.11550.032110.13730.775-3.103
152.91551.606-0.12028.2081-0.241210.8541-0.0070.225-0.1787-1.25020.3045-0.03961.5230.2083-0.29760.5838-0.1667-0.01810.1719-0.04750.02816.27423.0930.806
168.7745-0.9836-2.48543.51031.76527.5451-0.0947-0.20340.7046-0.39640.12581.0191-0.1781-1.042-0.03110.1984-0.1021-0.13990.33640.06950.3146-1.24734.47910.132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 591 - 28
2X-RAY DIFFRACTION2AA60 - 16829 - 137
3X-RAY DIFFRACTION3AA169 - 268138 - 237
4X-RAY DIFFRACTION4AA269 - 348238 - 317
5X-RAY DIFFRACTION5BB32 - 901 - 59
6X-RAY DIFFRACTION6BB91 - 15060 - 119
7X-RAY DIFFRACTION7BB151 - 221120 - 190
8X-RAY DIFFRACTION8BB222 - 348191 - 317
9X-RAY DIFFRACTION9CC60 - 9013 - 43
10X-RAY DIFFRACTION10CC91 - 12444 - 77
11X-RAY DIFFRACTION11CC125 - 14278 - 95
12X-RAY DIFFRACTION12CC143 - 19196 - 144
13X-RAY DIFFRACTION13DD60 - 9013 - 43
14X-RAY DIFFRACTION14DD91 - 13044 - 83
15X-RAY DIFFRACTION15DD131 - 15684 - 109
16X-RAY DIFFRACTION16DD157 - 191110 - 144

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