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- PDB-8oy1: Structure of the human Guanine Nucleotide-Binding Protein G(K) Su... -

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Basic information

Entry
Database: PDB / ID: 8oy1
TitleStructure of the human Guanine Nucleotide-Binding Protein G(K) Subunit Alpha
ComponentsGuanine nucleotide-binding protein G(i) subunit alpha-3
KeywordsSIGNALING PROTEIN / MODULATOR / GPCR
Function / homology
Function and homology information


negative regulation of adenylate cyclase activity / GTP metabolic process / dopamine receptor signaling pathway / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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 ...negative regulation of adenylate cyclase activity / GTP metabolic process / dopamine receptor signaling pathway / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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 / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / lysosomal membrane / cell division / GTPase activity / centrosome / nucleolus / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsMedrano, F.J. / Blanco, F.J. / Ferreras-Gutierrez, M.O.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-113225GB-I00 Spain
CitationJournal: To Be Published
Title: Structure of the human Guanine Nucleotide-Binding Protein G(K) Subunit Alpha
Authors: Ferreras-Gutierrez, M.O. / Medrano, F.J. / Blanco, F.J.
History
DepositionMay 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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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-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3362
Polymers36,8931
Non-polymers4431
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-7 kcal/mol
Surface area15190 Å2
Unit cell
Length a, b, c (Å)113.065, 113.065, 68.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Guanine nucleotide-binding protein G(i) subunit alpha-3 / G(i) alpha-3


Mass: 36892.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08754
#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
Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium MES at pH 6.5 containing 20% PEG 8000 and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.34→58.7 Å / Num. obs: 5841 / % possible obs: 94.9 % / Redundancy: 18.8 % / Biso Wilson estimate: 156.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.6
Reflection shellResolution: 3.342→3.52 Å / Num. unique obs: 292 / CC1/2: 0.79 / % possible all: 79

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Processing

Software
NameVersionClassification
PHENIXdev_4746refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→58.7 Å / SU ML: 0.4862 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2801 266 4.56 %
Rwork0.2046 5570 -
obs0.2082 5836 85.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.44 Å2
Refinement stepCycle: LAST / Resolution: 3.34→58.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 28 0 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132619
X-RAY DIFFRACTIONf_angle_d1.29983536
X-RAY DIFFRACTIONf_chiral_restr0.0592392
X-RAY DIFFRACTIONf_plane_restr0.0094448
X-RAY DIFFRACTIONf_dihedral_angle_d17.6705975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-4.210.39181100.30042216X-RAY DIFFRACTION69.64
4.21-58.70.26011560.18683354X-RAY DIFFRACTION99.97
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)
13.21163283571-2.183236744272.905355263973.02699516328-1.793208612493.487406726840.1394597875980.3668259976580.699892551157-0.0375274572558-0.0601717997942-0.3929979075120.4112635421990.243168888158-0.1397955796881.27706524056-0.2997836828120.1860389468761.40232391656-0.05873644558221.3521220532521.7680598199-32.3250928337-8.75291652101
25.69926913116-1.97097673006-1.524854080822.34808868764-0.01170111483263.66146869838-0.6153019185050.793782443854-0.221324281671-0.2262320584290.06751360832470.07899316856180.8206138512970.336325624440.4798636139451.4267126219-0.00486725677323-0.04674854239171.570784538680.0645466724711.3051486620721.6830629631-51.7469981241-5.53164809321
35.34026114391-4.458042244561.725229493932.687177803160.9768511520682.234394570630.0887581672310.3530467659030.6449553691450.0601867067555-0.763101574608-0.869259792411-0.6830245837680.2284572119130.1618408183651.39888607279-0.285466009816-0.06329065637851.628178021860.3259135464241.4229530133719.5726807209-24.4044768544-8.57459993645
47.24557707954-1.47330834732-0.1860718029656.34139301404-0.9031733219448.94399773768-1.12878197823-2.414689720181.565694973510.280581040031.318230667570.05554413539720.788831893107-1.73739795889-0.04586116634230.95101566114-0.0196005493861-0.1267998669891.82442522635-0.1831399127331.740580816891.98515499998-28.5301066048-8.1036763607
56.5104265523-3.7510930115-3.840648992136.458270026213.21827974873.38786621006-0.2140673040710.8456739902852.006386224740.9862593338530.5518136845630.5795387641920.592238582375-0.99244722224-0.2243434880970.859174586247-0.292945161016-0.276022991591.62607625193-0.18709156942.301092741223.32384192196-17.9951659217-13.8525551973
63.937867325861.12643605113-0.256383936074.650938008161.722272275153.73116489301-0.632566694323-0.561711992784-0.58178833374-0.2408359503850.3508970680011.156784320580.366995766259-0.5006486173160.4897079732991.42840403603-0.145796201271-0.3212132438861.590969101610.04040687625791.675900342230.328761132135-32.660089022-20.2514273591
75.269566697524.246832300931.791183669125.02416787486-1.086657210663.94199235731-0.499910530912.679584957461.5325811532-3.63380393249-0.276928199239-0.586004881199-0.583455569448-0.02449257393381.383625453322.306251445320.0460902103277-0.1930929483421.850947323520.6319353727651.0733719897414.3745636866-18.5574757458-24.6233638011
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 90 )33 - 901 - 58
22chain 'A' and (resid 91 through 163 )91 - 16359 - 131
33chain 'A' and (resid 164 through 212 )164 - 212132 - 180
44chain 'A' and (resid 213 through 254 )213 - 254181 - 222
55chain 'A' and (resid 255 through 270 )255 - 270223 - 238
66chain 'A' and (resid 271 through 328 )271 - 328239 - 296
77chain 'A' and (resid 329 through 347 )329 - 347297 - 315

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