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- PDB-3qi2: A Galpha P-loop mutation prevents transition to the activated sta... -

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Basic information

Entry
Database: PDB / ID: 3qi2
TitleA Galpha P-loop mutation prevents transition to the activated state: G42R bound to RGS14 GoLoco
Components
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
  • Regulator of G-protein signaling 14
KeywordsSIGNALING PROTEIN / RGS14 GoLoco / Ras-like domain / all-helical domain / GoLoco motif / arginine finger / lipoprotein / transducer / guanine nucleotide dissociation inhibitor / GTP binding / nucleotide binding / ADP-ribosylation
Function / homology
Function and homology information


zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / positive regulation of neurogenesis / spindle organization / nucleocytoplasmic transport / negative regulation of G protein-coupled receptor signaling pathway / GDP-dissociation inhibitor activity / platelet-derived growth factor receptor signaling pathway ...zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / positive regulation of neurogenesis / spindle organization / nucleocytoplasmic transport / negative regulation of G protein-coupled receptor signaling pathway / GDP-dissociation inhibitor activity / platelet-derived growth factor receptor signaling pathway / negative regulation of MAP kinase activity / G-protein alpha-subunit binding / long-term memory / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / GTPase activator activity / regulation of mitotic spindle organization / learning / chromosome segregation / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / visual learning / PML body / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / centriolar satellite / G-protein beta/gamma-subunit complex binding / spindle / long-term synaptic potentiation / spindle pole / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / mitotic cell cycle / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / G protein activity / response to oxidative stress / midbody / cell cortex / G alpha (i) signalling events / G alpha (s) signalling events / microtubule binding / dendritic spine / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / Extra-nuclear estrogen signaling / postsynaptic density / nuclear body / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / dendrite / centrosome / protein kinase binding / GTP binding / nucleolus / glutamatergic synapse / magnesium ion binding / Golgi apparatus / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / GI Alpha 1, domain 2-like ...RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Regulator of G-protein signaling 14 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.797 Å
AuthorsBosch, D.E. / Willard, F.S. / Kimple, A.J. / Miley, M.J. / Siderovski, D.P.
Citation
Journal: Plos Pathog. / Year: 2012
Title: A P-loop Mutation in Galpha Subunits Prevents Transition to the Active State: Implications for G-protein Signaling in Fungal Pathogenesis
Authors: Bosch, D.E. / Willard, F.S. / Ramanujam, R. / Kimple, A.J. / Willard, M.D. / Naqvi, N.I. / Siderovski, D.P.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Structure-based protocol for identifying mutations that enhance protein-protein binding affinities.
Authors: Sammond, D.W. / Eletr, Z.M. / Purbeck, C. / Kimple, R.J. / Siderovski, D.P. / Kuhlman, B.
#2: Journal: Nature / Year: 2002
Title: Structural determinants for GoLoco-induced inhibition of nucleotide release by Galpha subunits.
Authors: Kimple, R.J. / Kimple, M.E. / Betts, L. / Sondek, J. / Siderovski, D.P.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Sep 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
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
C: Regulator of G-protein signaling 14
D: Regulator of G-protein signaling 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4219
Polymers83,2514
Non-polymers1,1715
Water66737
1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
C: Regulator of G-protein signaling 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2575
Polymers41,6252
Non-polymers6313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-30 kcal/mol
Surface area16760 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
D: Regulator of G-protein signaling 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1654
Polymers41,6252
Non-polymers5392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-34 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.003, 131.018, 203.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 37531.750 Da / Num. of mol.: 2 / Fragment: alpha-i1 subunit, residues 31-354 / Mutation: G42R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: pLIC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P63096, EC: 3.6.5.1
#2: Protein/peptide Regulator of G-protein signaling 14 / RGS14


Mass: 4093.621 Da / Num. of mol.: 2 / Fragment: GoLoco motif peptide, residues 497-532 / Source method: obtained synthetically
Details: synthetic GoLoco motif peptide identical to human RGS14 497-532
References: UniProt: O43566

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Non-polymers , 4 types, 42 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Hanging drops were a 1:1 mixture of protein-peptide complex in buffer (10 mM Tris pH 7.5, 1 mM magnesium chloride, 5% (w/v) glycerol, 5 mM DTT) and well solution (1.7 M ammonium sulfate, 100 ...Details: Hanging drops were a 1:1 mixture of protein-peptide complex in buffer (10 mM Tris pH 7.5, 1 mM magnesium chloride, 5% (w/v) glycerol, 5 mM DTT) and well solution (1.7 M ammonium sulfate, 100 mM sodium acetate pH 5.0, 200 mM magnesium chloride, 10% (w/v) glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2010 / Details: custom
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.797→29.705 Å / Num. all: 23542 / Num. obs: 18462 / % possible obs: 78.42 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.89 Å2 / Net I/σ(I): 2
Reflection shellResolution: 2.797→2.944 Å / Mean I/σ(I) obs: 2 / % possible all: 31

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2om2

2om2


Resolution: 2.797→29.705 Å / SU ML: 0.41 / σ(F): 0.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 952 5.16 %random
Rwork0.1963 ---
obs0.2001 18462 78.42 %-
all-23542 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.758 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.9978 Å2-0 Å2-0 Å2
2---8.6468 Å20 Å2
3----18.6539 Å2
Refinement stepCycle: LAST / Resolution: 2.797→29.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 72 37 5714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025770
X-RAY DIFFRACTIONf_angle_d0.4637779
X-RAY DIFFRACTIONf_dihedral_angle_d10.2712124
X-RAY DIFFRACTIONf_chiral_restr0.032866
X-RAY DIFFRACTIONf_plane_restr0.001985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.797-2.94410.3845600.2853982X-RAY DIFFRACTION31
2.9441-3.12830.3232880.27941729X-RAY DIFFRACTION55
3.1283-3.36960.37631280.25012373X-RAY DIFFRACTION75
3.3696-3.70810.30111680.21182903X-RAY DIFFRACTION92
3.7081-4.24330.23811690.17933088X-RAY DIFFRACTION98
4.2433-5.34110.25331760.15993164X-RAY DIFFRACTION98
5.3411-29.70680.21791630.17283271X-RAY DIFFRACTION98
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)
10.91990.2079-1.07110.7085-0.22081.48340.07570.00510.3464-0.02190.2911-0.0076-0.1084-0.1301-0.2386-0.0003-0.01070.05430.1827-0.04560.0717-18.30317.667134.9945
21.5723-0.85840.26450.57060.1160.98540.0370.0070.0013-0.1741-0.0915-0.0466-0.3859-0.0849-0.00170.24390.03330.0240.15150.05460.2611-39.739532.557429.4469
30.0584-0.0188-0.12540.46820.18480.4421-0.02280.038-0.1536-0.06650.1149-0.3440.0010.0337-0.04960.0344-0.09750.02590.38280.02110.2333-14.229113.035228.7144
40.1301-0.14820.32580.5356-0.41481.6405-0.0738-0.0587-0.3545-0.05850.1499-0.07420.0635-0.5452-0.0980.0216-0.02560.02790.223-0.02950.1725-34.37475.582236.9441
50.142-0.05560.14540.19580.25260.69030.008-0.027-0.0035-0.05250.13450.0054-0.14040.3532-0.10130.1247-0.0671-0.04110.195-0.05390.1306-19.91338.491944.2361
60.13250.08920.10070.41470.06850.16610.08520.01280.05060.05020.14-0.08070.02920.0887-0.13140.43270.2988-0.02840.5387-0.29460.3037-15.875543.569211.1878
70.47910.0154-0.26470.58160.63261.0274-0.1544-0.1003-0.0282-0.0045-0.11140.24150.036-0.05880.14770.01360.00150.04060.0768-0.06410.0944-31.709260.881922.8035
80.32470.28870.33343.17261.95752.0283-0.10480.1744-0.27130.8710.065-0.0560.5188-0.0241-0.08360.40890.0783-0.01550.1537-0.18060.2085-16.394743.023812.7457
90.3877-0.4483-0.43940.87451.12341.5948-0.1638-0.0006-0.12420.1237-0.08880.08430.15780.06270.11030.50570.2074-0.1530.4246-0.17190.3765-3.982748.297513.6724
100.60120.1143-0.26550.09330.06980.4171-0.13370.6287-0.2358-0.07170.2866-0.12950.05970.2486-0.02760.01390.08670.08730.3887-0.2757-0.1-11.2757.05664.0906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 30:59)
2X-RAY DIFFRACTION2(chain A and resid 60:181)
3X-RAY DIFFRACTION3(chain A and resid 182:222)
4X-RAY DIFFRACTION4(chain A and resid 223:310)
5X-RAY DIFFRACTION5(chain A and resid 311:348)
6X-RAY DIFFRACTION6(chain B and resid 30:42)
7X-RAY DIFFRACTION7(chain B and resid 43:182)
8X-RAY DIFFRACTION8(chain B and resid 183:236)
9X-RAY DIFFRACTION9(chain B and resid 237:263)
10X-RAY DIFFRACTION10(chain B and resid 264:348)

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