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- PDB-3qe0: A Galpha-i1 P-loop mutation prevents transition to the activated state -

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Basic information

Entry
Database: PDB / ID: 3qe0
TitleA Galpha-i1 P-loop mutation prevents transition to the activated state
Components
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
  • KB752 peptide
KeywordsSIGNALING PROTEIN / KB752 / Ras-like domain / all-helical domain / arginine finger / lipoprotein / transducer / GTPase activity / GTP binding / nucleotide binding / ADP-ribosylation
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Structure / Year: 2005
Title: Structure of Galpha(i1) bound to a GDP-selective peptide provides insight into guanine nucleotide exchange.
Authors: Johnston, C.A. / Willard, F.S. / Jezyk, M.R. / Fredericks, Z. / Bodor, E.T. / Jones, M.B. / Blaesius, R. / Watts, V.J. / Harden, T.K. / Sondek, J. / Ramer, J.K. / Siderovski, D.P.
History
DepositionJan 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Guanine nucleotide-binding protein G(i) subunit alpha-1
G: KB752 peptide
F: KB752 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,21611
Polymers115,8145
Non-polymers1,4036
Water21612
1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
F: KB752 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7514
Polymers39,2842
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-29 kcal/mol
Surface area15810 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
G: KB752 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7514
Polymers39,2842
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-30 kcal/mol
Surface area15780 Å2
MethodPISA
3
C: Guanine nucleotide-binding protein G(i) subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7143
Polymers37,2461
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.637, 106.637, 455.062
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 34:109 or resseq 121:176 or resseq...
211chain B and (resseq 34:109 or resseq 121:176 or resseq...
311chain C and (resseq 34:109 or resseq 121:176 or resseq...

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Components

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


Mass: 37246.422 Da / Num. of mol.: 3 / Fragment: alpha-i1 subunit, residues 33-354 / 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 KB752 peptide


Mass: 2037.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic phage display peptide
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Hanging drops were a 1:1 mixture of protein-peptide complex in buffer (50 mM HEPES pH 8.0, 10 mM magnesium chloride, 10 microM GppNHp, 1 mM EDTA, 5 mM DTT) and well solution (17% (w/v) PEG ...Details: Hanging drops were a 1:1 mixture of protein-peptide complex in buffer (50 mM HEPES pH 8.0, 10 mM magnesium chloride, 10 microM GppNHp, 1 mM EDTA, 5 mM DTT) and well solution (17% (w/v) PEG MME 5K, 200 mM magnesium chloride, 100 mM HEPES pH 7.0), 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: Oct 1, 2010 / Details: custom
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→39.441 Å / Num. all: 31834 / Num. obs: 30772 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 68.596 Å2
Reflection shellResolution: 3→3.03 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 1255 / % possible all: 85.4

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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: PDB entry 1Y3A

1y3a


Resolution: 3→39.441 Å / SU ML: 0.45 / σ(F): 1.36 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2917 1555 5.05 %random
Rwork0.2469 ---
obs0.2491 30770 96.66 %-
all-31834 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.431 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7957 Å2-0 Å20 Å2
2---1.7957 Å2-0 Å2
3---3.5914 Å2
Refinement stepCycle: LAST / Resolution: 3→39.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7631 0 87 12 7730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027857
X-RAY DIFFRACTIONf_angle_d0.54610597
X-RAY DIFFRACTIONf_dihedral_angle_d12.1642853
X-RAY DIFFRACTIONf_chiral_restr0.0361180
X-RAY DIFFRACTIONf_plane_restr0.0011327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2130X-RAY DIFFRACTIONPOSITIONAL
12B2130X-RAY DIFFRACTIONPOSITIONAL0.012
13C2130X-RAY DIFFRACTIONPOSITIONAL0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0032-3.11050.40591780.35092742X-RAY DIFFRACTION95
3.1105-3.2350.3781380.32342906X-RAY DIFFRACTION97
3.235-3.38210.36191340.30322862X-RAY DIFFRACTION97
3.3821-3.56030.34021560.28052924X-RAY DIFFRACTION98
3.5603-3.78320.30391680.25582861X-RAY DIFFRACTION97
3.7832-4.07510.28931380.23352920X-RAY DIFFRACTION97
4.0751-4.48460.241580.19682917X-RAY DIFFRACTION97
4.4846-5.13240.21981700.19142929X-RAY DIFFRACTION97
5.1324-6.46170.28791570.24142980X-RAY DIFFRACTION97
6.4617-39.4440.28411580.24183174X-RAY DIFFRACTION95
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)
10.6960.70610.38730.64030.34971.1350.30840.04440.04430.25930.0110.33650.22390.0798-0.28690.24790.0446-0.00630.0985-0.03780.301247.3629-21.2829-8.9091
20.89210.1623-0.49280.6594-0.40220.3866-0.14010.6438-0.0482-0.44860.2249-0.11550.0953-0.25420.03930.54180.12840.16210.25060.13570.118464.1299-16.8228-15.783
30.88990.2365-0.55690.2019-0.53812.1772-0.09090.0279-0.0281-0.1449-0.01-0.0633-0.71150.0353-0.2170.4845-0.06140.14930.31360.14240.174859.31651.7496-26.4101
40.6339-0.5077-0.08571.262-0.41992.54990.17320.0657-0.2953-0.2253-0.46060.22350.67380.52630.13560.27620.0578-0.05240.11650.01180.211951.9574-21.1397-13.1415
51.0969-0.73870.74150.5556-0.3341.2460.0495-0.0071-0.01520.0205-0.04690.2893-0.2955-0.37060.07460.0569-0.0349-0.10650.0881-0.04130.164235.4048-8.3568-12.009
60.09810.13140.31211.3298-0.68191.2132-0.1375-0.22110.25650.03860.01660.33670.0938-0.17070.02380.11960.0107-0.06230.1362-0.06780.237337.0595-16.7169-0.5255
73.28270.75592.41250.80220.53123.77690.0642-0.20590.1707-0.05870.17190.12750.6845-1.0857-0.10280.2715-0.4129-0.11790.6581-0.04290.163930.0985-30.43768.7125
81.2113-0.302-0.75470.95560.20432.0573-0.32120.00460.07860.07050.072-0.03330.20370.32940.17090.23-0.10810.05050.28140.00330.174827.8027-40.728414.8544
91.58451.3471-0.58061.2769-0.92681.25450.4254-0.22990.33010.4845-0.06580.2761-0.70150.1691-0.11120.4939-0.15750.15740.1078-0.12250.215430.081-18.041128.5101
102.94070.9598-1.05920.6391-0.70341.3492-0.63020.2445-0.2213-0.17840.2687-0.16750.5169-0.40680.29560.355-0.16550.07290.288-0.06030.191528.5607-41.331210.297
111.30610.6461-0.43150.7284-0.41660.2516-0.6340.45440.1964-0.20470.331-0.1237-0.16470.12640.21020.4098-0.3567-0.15830.45370.11550.291914.5792-38.35856.1013
121.48660.46570.4220.42770.19650.13-0.4623-0.22420.1627-0.23720.64310.33-0.1214-0.2294-0.12090.2376-0.3277-0.05680.45970.06080.360916.894-39.662622.4413
133.4480.14432.48812.7567-0.46281.9075-0.356-0.43650.8902-0.15820.47320.74020.269-0.6967-0.24890.0172-0.15780.16870.63680.28610.51798.2712-31.519626.6228
141.40440.84631.02291.18710.1111.3388-0.5444-0.38240.0940.15090.1254-0.02830.3065-1.0119-0.347-0.089-0.4530.16290.31690.1490.125918.2744-46.910426.8019
150.5519-0.13331.07251.049-0.07281.0469-0.08210.1810.10040.0481-0.29540.162-0.3910.40240.26150.61580.1612-0.04690.52660.05030.329472.8039-28.999212.5533
162.4459-1.4558-0.36694.3002-1.76321.5033-0.3463-0.3486-0.20780.9363-0.41680.4088-0.15230.26610.29070.3740.26020.05250.4643-0.01230.020463.2828-37.929110.0212
171.02071.17490.15221.36020.24530.4349-0.2314-0.21820.4559-0.2064-0.2279-0.0634-0.67010.12090.52060.71470.2935-0.21520.3109-0.00430.786572.4261-22.985413.18
180.6320.4742-0.0431.0931-1.54633.0861-0.10350.12390.28420.3453-0.5416-0.2183-0.24480.45640.57541.2-0.2311-0.14150.85630.35540.763587.4681-11.388920.7847
196.67082.91470.66393.2481.24772.86140.13491.44130.39880.29790.12420.42530.23331.0441-0.22220.8720.21270.3361.34080.18911.34297.0205-23.112210.0222
200.4060.3121.08040.46211.13423.2438-0.13460.43360.1407-0.40340.11080.0383-0.44191.2340.1320.58040.27970.03321.13730.2720.21588.7997-33.743120.6317
210.5349-0.04220.84320.22460.29762.1426-0.2029-0.29480.04030.2802-0.3053-0.057-0.32580.20060.38070.50130.1117-0.04750.76290.24710.369988.897-30.978529.2322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 32:59)
2X-RAY DIFFRACTION2(chain A and resid 60:77)
3X-RAY DIFFRACTION3(chain A and resid 78:159)
4X-RAY DIFFRACTION4(chain A and resid 160:212)
5X-RAY DIFFRACTION5(chain A and resid 213:307)
6X-RAY DIFFRACTION6(chain A and resid 308:348)
7X-RAY DIFFRACTION7(chain A and resid 349:354)
8X-RAY DIFFRACTION8(chain B and resid 32:60)
9X-RAY DIFFRACTION9(chain B and resid 61:176)
10X-RAY DIFFRACTION10(chain B and resid 177:197)
11X-RAY DIFFRACTION11(chain B and resid 198:215)
12X-RAY DIFFRACTION12(chain B and resid 216:235)
13X-RAY DIFFRACTION13(chain B and resid 236:245)
14X-RAY DIFFRACTION14(chain B and resid 246:347)
15X-RAY DIFFRACTION15(chain C and resid 34:101)
16X-RAY DIFFRACTION16(chain C and resid 102:165)
17X-RAY DIFFRACTION17(chain C and resid 166:185)
18X-RAY DIFFRACTION18(chain C and resid 186:201)
19X-RAY DIFFRACTION19(chain C and resid 202:215)
20X-RAY DIFFRACTION20(chain C and resid 216:246)
21X-RAY DIFFRACTION21(chain C and resid 247:347)

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