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- PDB-6m8h: Crystal Structure of the R208Q mutant of G(i) subunit alpha-1 -

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Basic information

Entry
Database: PDB / ID: 6m8h
TitleCrystal Structure of the R208Q mutant of G(i) subunit alpha-1
ComponentsGuanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsSIGNALING PROTEIN / G protein / Switch II region / Oncogenic Mutation
Function / homology
Function and homology information


Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / 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 / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / nucleus / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsMascarenhas, R. / Goossens, J. / Leverson, B. / Kothawala, S. / Ballicora, M. / Olsen, K. / de freitas, D. / Liu, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM112025 United States
CitationJournal: To Be Published
Title: FUNCTIONAL CONSEQUENCES OF ONCOGENIC MUTATIONS IN THE SWITCH II REGION OF Galphai1 and Galphas PROTEINS
Authors: Goossens, J.L. / Leverson, B.D. / Kothawala, S. / Mascarenhas, R. / Liu, D. / Ballicora, M. / Olsen, K.W. / de Freitas, D.M.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)40,9343
Polymers40,3701
Non-polymers5642
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-18 kcal/mol
Surface area14750 Å2
Unit cell
Length a, b, c (Å)79.558, 79.558, 105.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 40369.965 Da / Num. of mol.: 1 / Mutation: R208Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai1, Gnai-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10824
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 297 K / Method: evaporation / Details: 2.0 M (NH4)2SO3 pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 24084 / % possible obs: 100 % / Redundancy: 10.7 % / Net I/σ(I): 33.1
Reflection shellResolution: 2.11→5.62 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.07→41.864 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 2907 8.45 %
Rwork0.1653 --
obs0.1681 34409 75.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→41.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 33 211 2764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042644
X-RAY DIFFRACTIONf_angle_d0.5973577
X-RAY DIFFRACTIONf_dihedral_angle_d8.2522191
X-RAY DIFFRACTIONf_chiral_restr0.042399
X-RAY DIFFRACTIONf_plane_restr0.002451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0704-2.10440.256650.2198647X-RAY DIFFRACTION33
2.1044-2.14070.2434740.2095786X-RAY DIFFRACTION40
2.1407-2.17960.2732940.2261965X-RAY DIFFRACTION50
2.1796-2.22150.25751030.21771083X-RAY DIFFRACTION54
2.2215-2.26690.25321000.20781089X-RAY DIFFRACTION55
2.2669-2.31610.21931040.19631120X-RAY DIFFRACTION57
2.3161-2.370.28881130.19741180X-RAY DIFFRACTION60
2.37-2.42930.21621070.18661243X-RAY DIFFRACTION63
2.4293-2.4950.22121120.18681330X-RAY DIFFRACTION66
2.495-2.56840.21361380.18071383X-RAY DIFFRACTION69
2.5684-2.65130.22991380.18891476X-RAY DIFFRACTION74
2.6513-2.7460.23251530.17521556X-RAY DIFFRACTION80
2.746-2.85590.20821640.17911783X-RAY DIFFRACTION90
2.8559-2.98590.22711820.16541944X-RAY DIFFRACTION99
2.9859-3.14320.22561840.16642008X-RAY DIFFRACTION100
3.1432-3.34010.16631780.16651966X-RAY DIFFRACTION100
3.3401-3.59790.17691860.15991994X-RAY DIFFRACTION100
3.5979-3.95970.17871700.13611980X-RAY DIFFRACTION100
3.9597-4.5320.14641770.13721994X-RAY DIFFRACTION100
4.532-5.70760.16911870.14731975X-RAY DIFFRACTION100
5.7076-41.87280.20721780.16962000X-RAY DIFFRACTION100

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