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- PDB-3r7w: Crystal Structure of Gtr1p-Gtr2p complex -

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Basic information

Entry
Database: PDB / ID: 3r7w
TitleCrystal Structure of Gtr1p-Gtr2p complex
Components
  • GTP-binding protein GTR1
  • GTP-binding protein GTR2
KeywordsPROTEIN TRANSPORT / Rag GTPases / Gtr1p / Gtr2p / mTOR
Function / homology
Function and homology information


MTOR signalling / protein localization to vacuolar membrane / Gtr1-Gtr2 GTPase complex / Ragulator complex / phosphate ion transport / microautophagy / Amino acids regulate mTORC1 / endocytic recycling / fungal-type vacuole membrane / transcription by RNA polymerase I ...MTOR signalling / protein localization to vacuolar membrane / Gtr1-Gtr2 GTPase complex / Ragulator complex / phosphate ion transport / microautophagy / Amino acids regulate mTORC1 / endocytic recycling / fungal-type vacuole membrane / transcription by RNA polymerase I / transcription by RNA polymerase III / positive regulation of TOR signaling / subtelomeric heterochromatin formation / positive regulation of TORC1 signaling / cellular response to starvation / negative regulation of autophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / late endosome / late endosome membrane / chromosome, telomeric region / GTPase activity / chromatin / GTP binding / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Beta-Lactamase - #190 / RagA/B / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Beta-Lactamase - #190 / RagA/B / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTP-binding protein GTR2 / GTP-binding protein GTR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.773 Å
AuthorsGong, R. / Li, L. / Liu, Y. / Wang, P. / Yang, H. / Wang, L. / Cheng, J. / Guan, K.L. / Xu, Y.
CitationJournal: Genes Dev. / Year: 2011
Title: Crystal structure of the Gtr1p-Gtr2p complex reveals new insights into the amino acid-induced TORC1 activation
Authors: Gong, R. / Li, L. / Liu, Y. / Wang, P. / Yang, H. / Wang, L. / Cheng, J. / Guan, K.L. / Xu, Y.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein GTR1
B: GTP-binding protein GTR2
C: GTP-binding protein GTR1
D: GTP-binding protein GTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,39512
Polymers148,2094
Non-polymers2,1868
Water724
1
A: GTP-binding protein GTR1
B: GTP-binding protein GTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1976
Polymers74,1042
Non-polymers1,0934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area27550 Å2
MethodPISA
2
C: GTP-binding protein GTR1
D: GTP-binding protein GTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1976
Polymers74,1042
Non-polymers1,0934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-21 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.908, 148.439, 98.508
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein GTR1 / Gtpase1


Mass: 36036.566 Da / Num. of mol.: 2 / Fragment: residues 8-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GTR1 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q00582
#2: Protein GTP-binding protein GTR2 / Gtpase2


Mass: 38067.758 Da / Num. of mol.: 2 / Fragment: residues 11-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GTR2 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53290
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 46969 / % possible obs: 95.1 % / Biso Wilson estimate: 73.31 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.773→44.06 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 36.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 2288 4.88 %
Rwork0.2357 --
obs0.2382 46857 95.02 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.489 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 228.52 Å2 / Biso mean: 97.2195 Å2 / Biso min: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.246 Å2-0 Å220.2737 Å2
2--3.8796 Å2-0 Å2
3---2.3664 Å2
Refinement stepCycle: LAST / Resolution: 2.773→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8875 0 132 4 9011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02310019
X-RAY DIFFRACTIONf_angle_d1.52113123
X-RAY DIFFRACTIONf_chiral_restr0.0991501
X-RAY DIFFRACTIONf_plane_restr0.0051628
X-RAY DIFFRACTIONf_dihedral_angle_d24.8025948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7729-2.83320.306720.33691106110836
2.8332-2.89910.3285266086
2.8991-2.97160.31523085100
2.9716-3.05190.36125260.307624793005100
3.0519-3.14170.29583112100
3.1417-3.24310.28993038100
3.2431-3.3590.3244790.274325903069100
3.359-3.49340.26153095100
3.4934-3.65230.24563054100
3.6523-3.84480.28644110.234926683079100
3.8448-4.08550.22063092100
4.0855-4.40070.19993070100
4.4007-4.8430.24473910.189426923083100
4.843-5.54270.2413085100
5.5427-6.97870.373070.255928103117100
6.9787-44.06560.21421720.20462933310599

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