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- PDB-8vgb: Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Sub... -

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Basic information

Entry
Database: PDB / ID: 8vgb
TitleCrystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) from Oryza sativa in complex with GDP
ComponentsGuanine nucleotide-binding protein alpha-1 subunit
KeywordsSIGNALING PROTEIN / G Protein / Alpha Subunit / OsGPA / Oryza sativa
Function / homology
Function and homology information


defense response / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / heterotrimeric G-protein complex / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Plant G-protein, alpha subunit / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein alpha-1 subunit
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLee, S.G. / Jez, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structure-function analysis of plant G-protein regulatory mechanisms identifies key G alpha-RGS protein interactions.
Authors: Torres-Rodriguez, M.D. / Lee, S.G. / Roy Choudhury, S. / Paul, R. / Selvam, B. / Shukla, D. / Jez, J.M. / Pandey, S.
History
DepositionDec 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 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 alpha-1 subunit
B: Guanine nucleotide-binding protein alpha-1 subunit
C: Guanine nucleotide-binding protein alpha-1 subunit
D: Guanine nucleotide-binding protein alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,86912
Polymers177,9994
Non-polymers1,8708
Water00
1
A: Guanine nucleotide-binding protein alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9673
Polymers44,5001
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanine nucleotide-binding protein alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9673
Polymers44,5001
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Guanine nucleotide-binding protein alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9673
Polymers44,5001
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Guanine nucleotide-binding protein alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9673
Polymers44,5001
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.393, 68.419, 167.977
Angle α, β, γ (deg.)90.000, 89.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Guanine nucleotide-binding protein alpha-1 subunit / GP-alpha-1 / Protein Dwarf1


Mass: 44499.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Gene: GPA1, D1, GA1, RGA1, OsI_018808 / Production host: Escherichia coli (E. coli) / References: UniProt: A2Y3B5
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM sodium acetate trihydrate (pH 8.5), 100 mM Tris (pH 8.5), 30% (w/v) PEG-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 31650 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.061 / Rsym value: 0.036 / Net I/σ(I): 26.44
Reflection shellResolution: 2.99→3.04 Å / Mean I/σ(I) obs: 1.94 / Num. unique obs: 1586 / CC1/2: 0.744 / CC star: 0.924 / Rpim(I) all: 0.362 / Rrim(I) all: 0.711 / Rsym value: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-30001.20.1_4487data collection
PHASERphasing
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→48.37 Å / Cross valid method: FREE R-VALUE / σ(F): 5.38 / Phase error: 32.9117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3061 2079 6.88 %
Rwork0.266 28135 -
obs0.269 30214 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.83 Å2
Refinement stepCycle: LAST / Resolution: 2.99→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9801 0 116 0 9917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005110100
X-RAY DIFFRACTIONf_angle_d1.091113586
X-RAY DIFFRACTIONf_chiral_restr0.05271494
X-RAY DIFFRACTIONf_plane_restr0.00581674
X-RAY DIFFRACTIONf_dihedral_angle_d9.47771314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.070.37551140.32951750X-RAY DIFFRACTION77.61
3.07-3.150.39931320.33251840X-RAY DIFFRACTION81.78
3.15-3.240.35091350.34051932X-RAY DIFFRACTION84.85
3.24-3.350.34861350.3171904X-RAY DIFFRACTION86
3.35-3.470.31321350.31141972X-RAY DIFFRACTION87.96
3.47-3.610.33341390.28852096X-RAY DIFFRACTION90.78
3.61-3.770.32071370.27471996X-RAY DIFFRACTION91.27
3.77-3.970.27571410.282096X-RAY DIFFRACTION92.01
3.97-4.220.29871440.26942090X-RAY DIFFRACTION92.15
4.22-4.540.37921330.24162095X-RAY DIFFRACTION93.07
4.54-50.28241490.24432062X-RAY DIFFRACTION91.81
5-5.720.25461460.26952154X-RAY DIFFRACTION92.92
5.72-7.20.40681470.27242100X-RAY DIFFRACTION92.63
7.21-48.370.26181450.23232195X-RAY DIFFRACTION92.66
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)
12.238579986470.9518048106191.116436229271.157721205-0.4719021555952.247232013950.34950585492-0.271099063709-0.06579072187140.323237055672-0.182214193529-0.5102623060540.1241237641170.21223646808-0.338610092020.838284914467-0.054301753122-0.04763758971540.53790846989-0.02097014943450.550399127714-57.0919063699-203.11047957666.5080998281
24.454405288940.754735245488-1.189286385612.14241347648-0.3022845144282.705135471120.438662679797-0.1015873748250.7895968011010.176944096391-0.137493443184-0.006645725172940.0794835080175-0.0454416669863-0.2361533483331.031316329620.01162423928910.227428390380.282746206748-0.02975007137790.509208280648-64.1993657656-187.01493911645.8808850272
32.000538812661.11360589564-0.3233986719630.629329033039-0.4402928383223.40195390230.09552755366010.02538266945820.0491448417130.531453464566-0.3495067479140.2881971958890.0479926182888-0.617990949899-0.352825108320.749088784395-0.1422086230890.1101416287540.9801732320560.01855831092520.403319562772-84.5649940578-205.09753216767.9491237068
41.05941483167-0.9157356128760.8202497455352.14805338242-1.54467997571.09025896036-0.1428853977030.02735236107390.0769407078594-0.3362786544010.0261905791022-0.251841677940.3159376066430.3162326241410.06439688630130.785522192254-0.171586912756-0.08098874865490.602305310742-0.05476910107020.644291189077-69.9837753741-224.59704530257.9167146578
52.668506044330.61580368099-1.181884648925.18111759157-1.163251916474.68147362591-0.105739295093-0.05116153441740.0653544256167-0.0545753092330.392645939020.410148127109-0.0768735975854-0.0853414393259-0.3268826253470.4280250652630.031493894227-0.01751765241420.5729037315710.08879500044470.354209755342-87.6549907281-210.78208151780.3233652389
61.42912226017-0.19426321222-0.1506454527281.80075145596-1.085567395441.937869357910.4640910365580.0519718163730.24178261324-0.0454953320994-0.2075051640750.1718873833360.0127964985671-0.08912815790550.04009992985521.012236171540.1225291689260.2477904715260.382445442186-0.05164712335760.51836024747-98.375278339-216.83932690320.2185428809
73.14991529320.3745062574390.991099682993.025230639751.757823960571.30774109472-0.106354409269-0.1428141125270.727850784804-0.7619297128440.0742952204328-0.863830463264-0.3594188279810.0964034789752-0.2073512803990.969092645404-0.03420061600560.1085834891220.733441795088-0.08286383350240.832980747689-81.7491211741-206.34624281115.5382468917
83.674898797641.22005838287-1.409057919850.530586454299-0.4128089706860.576357302054-0.4196254683360.593613409561-0.9540407305070.4656804774760.213141480628-0.422024278808-0.388272755372-0.987116811402-0.08481684616271.092519416810.294470202899-0.1139839929260.692130966889-0.06616573720640.491660294435-93.7547771649-218.37227412514.820394742
94.3074737356-0.901405062351.318927755081.235621732090.373599473293.888306546320.736277938011-0.1973121534790.22542446813-0.00476944115328-0.1688152944590.167948233175-0.274147828725-0.431035822509-0.2419055457710.990046158291-0.0131306747677-0.1079956499830.3403261588280.01388578628510.477655494921-102.187211368-223.20596959137.6187635393
104.91333983958-0.4268988897930.4114727208972.46236583119-0.3518109350041.794996035170.555400444648-0.204112300677-1.02540756318-0.15231479691-0.1921664194030.1972735421820.3802202408530.105065042947-0.171272464641.069929675810.0141903755571-0.1614883709420.242269533720.0142699395510.673958521536-96.2087846389-233.70911797339.0046549873
111.641431918191.06120670828-0.1463509711920.940100020917-0.4959325945662.547600362620.07629076443860.02039662440090.1513538956520.3098031682840.0735463162422-0.06037045781950.02683546856080.265484610677-0.161924693330.580343182970.268050318952-0.002053649689260.610400358064-0.01669551850050.577318954865-40.1617337438-199.85005008421.4465899831
122.23096203028-1.576307072630.7634614486054.9342873177-1.145958664125.05005744729-0.21275154375-0.399935546803-0.19345471826-0.1193796797130.6472031674540.618157306842-0.232629990899-0.296702324001-0.3258635935730.441710744327-0.02068837496560.06577154272480.6709779259560.1690534192530.385528213211-55.4704115819-201.6487725262.69279397666
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 40 through 197 )AA40 - 1971 - 145
22chain 'A' and (resid 198 through 375 )AA198 - 375146 - 288
33chain 'B' and (resid 39 through 72 )BD39 - 721 - 26
44chain 'B' and (resid 73 through 195 )BD73 - 19527 - 133
55chain 'B' and (resid 196 through 375 )BD196 - 375134 - 296
66chain 'C' and (resid 40 through 99 )CG40 - 991 - 60
77chain 'C' and (resid 100 through 163 )CG100 - 16361 - 112
88chain 'C' and (resid 164 through 197 )CG164 - 197113 - 146
99chain 'C' and (resid 198 through 289 )CG198 - 289147 - 212
1010chain 'C' and (resid 290 through 375 )CG290 - 375213 - 293
1111chain 'D' and (resid 40 through 238 )DJ40 - 2381 - 172
1212chain 'D' and (resid 239 through 375 )DJ239 - 375173 - 299

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