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- PDB-3ums: Crystal structure of the G202A mutant of human G-alpha-i1 -

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Basic information

Entry
Database: PDB / ID: 3ums
TitleCrystal structure of the G202A mutant of human G-alpha-i1
ComponentsGuanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsCELL CYCLE / GTPASE / G-PROTEIN / HYDROLYSIS / HYDROLASE
Function / homology
Function and homology information


Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding ...Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.343 Å
AuthorsLambert, N.A. / Johnston, C.A. / Cappell, S.D. / Kuravi, S. / Kimple, A.J. / Willard, F.S. / Siderovski, D.P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Correction for Regulators of G-protein Signaling accelerate GPCR signaling kinetics and govern sensitivity solely by accelerating GTPase activity
Authors: Lambert, N.A. / Johnston, C.A. / Cappell, S.D. / Kuravi, S. / Kimple, A.J. / Willard, F.S. / Siderovski, D.P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Regulators of G-protein signaling accelerate GPCR signaling kinetics and govern sensitivity solely by accelerating GTPase activity.
Authors: Lambert, N.A. / Johnston, C.A. / Cappell, S.D. / Kuravi, S. / Kimple, A.J. / Willard, F.S. / Siderovski, D.P.
History
DepositionNov 14, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2012ID: 2PZ2
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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: Guanine nucleotide-binding protein G(i) subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0044
Polymers40,4291
Non-polymers5753
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.531, 121.531, 67.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 40429.059 Da / Num. of mol.: 1 / Mutation: G202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: PPRO-EXHTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P63096
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: Protein: 10-20 mg/mL in 50 mM HEPES, pH 8.0, 1 mM EDTA, 100 microM GDP, 5 mM DTT, well solution: 1.8-2.2 M ammonium sulfate, 0.1M sodium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 12, 2007
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.34→31.58 Å / Num. all: 19799 / Num. obs: 19799 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 46.56 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 27.7
Reflection shellResolution: 2.34→2.36 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 2 / Num. unique all: 341 / % possible all: 67.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: dev_887)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GDD

1gdd


Resolution: 2.343→31.579 Å / SU ML: 0.4 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1183 5.98 %Random
Rwork0.1803 ---
obs0.1831 19792 94.58 %-
all-19792 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.641 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.343→31.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 34 126 2850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082774
X-RAY DIFFRACTIONf_angle_d1.0783743
X-RAY DIFFRACTIONf_dihedral_angle_d14.7321031
X-RAY DIFFRACTIONf_chiral_restr0.057417
X-RAY DIFFRACTIONf_plane_restr0.003477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.343-2.45010.38891420.32021895203779
2.4501-2.57920.3641420.27452352249295
2.5792-2.74070.28411350.24972330246596
2.7407-2.95220.25451450.20442366251196
2.9522-3.2490.25571610.20382371253297
3.249-3.71850.22621490.18392403255297
3.7185-4.68250.18321660.13752396256298
4.6825-31.58170.19041430.1512496263998
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)
14.93431.8154-3.27312.2406-1.69835.20020.0486-0.1301-0.25890.2192-0.1568-0.2787-0.0225-0.05040.07230.28560.0423-0.04610.32750.00750.4209-45.302428.241816.5164
26.4009-3.9548-1.06453.50340.08971.71690.08610.074-0.673-0.3112-0.21360.06870.2701-0.13370.1230.3550.00140.01390.26460.01520.3687-21.956929.60682.5317
35.59543.3385-1.35197.7191-1.99082.8520.13960.21810.37460.0888-0.0038-0.0062-0.19120.1504-0.15270.20720.0230.02750.3685-0.01910.22670.369139.7446-11.3823
48.86540.4655-3.77279.33-2.23183.9647-0.1777-0.1567-0.3980.11290.2611-0.90660.60131.0081-0.03910.22610.06440.05490.41870.01460.26152.787332.7296-7.6862
54.47740.5844-2.43244.5803-1.3853.73970.0632-0.4398-0.06410.1778-0.0290.1869-0.07750.2735-0.05420.27540.03110.02220.3687-0.04030.2498-6.308137.5737-1.4521
64.00661.7434-1.54873.5573-0.21852.4959-0.18550.3914-0.0854-0.62210.20040.09980.0056-0.2490.03420.31470.03670.00090.3799-0.02560.2396-31.640835.91612.3265
76.5953-1.922-1.81960.55710.53030.50320.53252.19250.0136-1.69970.76250.2501-0.32460.87260.31781.4355-0.199-0.01871.0883-0.06340.4062-19.123553.0682-10.9523
87.31831.4366-1.01275.62770.70314.2997-0.14510.35290.8273-0.4793-0.02490.6744-0.2342-0.41930.1250.36850.0171-0.04030.3296-0.0280.3394-29.244348.31392.4531
97.853.8070.71987.47930.60322.24020.24-0.0530.8975-0.1252-0.2480.4298-0.2001-0.02310.01240.41860.05080.06610.2341-0.040.3048-21.684658.34676.663
101.26281.6999-1.26683.27-1.06041.64020.196-0.41960.32030.1896-0.0740.325-0.1440.1054-0.06080.3210.02490.010.3103-0.06650.2765-34.017139.726512.1005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:36)
2X-RAY DIFFRACTION2(chain A and resid 37:68)
3X-RAY DIFFRACTION3(chain A and resid 69:114)
4X-RAY DIFFRACTION4(chain A and resid 115:132)
5X-RAY DIFFRACTION5(chain A and resid 133:181)
6X-RAY DIFFRACTION6(chain A and resid 182:231)
7X-RAY DIFFRACTION7(chain A and resid 232:242)
8X-RAY DIFFRACTION8(chain A and resid 243:278)
9X-RAY DIFFRACTION9(chain A and resid 279:312)
10X-RAY DIFFRACTION10(chain A and resid 313:354)

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