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- PDB-4arz: The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP -

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Basic information

Entry
Database: PDB / ID: 4arz
TitleThe crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP
Components(GTP-BINDING PROTEIN ...G protein) x 2
KeywordsHYDROLASE / GTPASE / CELL GROWTH
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 / subtelomeric heterochromatin formation ...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 / subtelomeric heterochromatin formation / positive regulation of TOR signaling / transcription by RNA polymerase I / transcription by RNA polymerase III / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / GTP-binding protein GTR2 / GTP-binding protein GTR1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.1 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of the Gtr1Pgtp-Gtr2Pgdp Complex Reveals Large Structural Rearrangements Triggered by GTP-to-Gdp Conversion
Authors: Jeong, J.H. / Lee, K.H. / Kim, Y.M. / Kim, D.H. / Oh, B.H. / Kim, Y.G.
History
DepositionApr 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5175
Polymers74,5262
Non-polymers9913
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-38.1 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.712, 148.897, 117.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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GTP-BINDING PROTEIN ... , 2 types, 2 molecules AB

#1: Protein GTP-BINDING PROTEIN GTR1


Mass: 35892.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00582
#2: Protein GTP-BINDING PROTEIN GTR2


Mass: 38633.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53290

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Non-polymers , 4 types, 12 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97928
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 14921 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.53
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER / Resolution: 3.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 1264 4.5 %RANDOM
Rwork0.225 ---
obs0.225 14921 92.5 %-
Solvent computationBsol: 42.4489 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.143 Å20 Å20 Å2
2--19.268 Å20 Å2
3----36.411 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 61 9 4870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0099
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.695
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOPOL
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOPOL
X-RAY DIFFRACTION3ION.PARAMION.TOPOL
X-RAY DIFFRACTION4GDP.PARGDP.TOPOL
X-RAY DIFFRACTION5GTP.PARGTP.TOPOL

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