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- PDB-4o2l: Structure of Mus musculus Rheb G63A mutant bound to GTP -

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Basic information

Entry
Database: PDB / ID: 4o2l
TitleStructure of Mus musculus Rheb G63A mutant bound to GTP
ComponentsGTP-binding protein Rheb
KeywordsHYDROLASE / Small GTPase / GDP and GTP
Function / homology
Function and homology information


Energy dependent regulation of mTOR by LKB1-AMPK / Amino acids regulate mTORC1 / MTOR signalling / Regulation of PTEN gene transcription / Macroautophagy / TP53 Regulates Metabolic Genes / mTORC1-mediated signalling / regulation of type B pancreatic cell development / regulation of TOR signaling / negative regulation of cold-induced thermogenesis ...Energy dependent regulation of mTOR by LKB1-AMPK / Amino acids regulate mTORC1 / MTOR signalling / Regulation of PTEN gene transcription / Macroautophagy / TP53 Regulates Metabolic Genes / mTORC1-mediated signalling / regulation of type B pancreatic cell development / regulation of TOR signaling / negative regulation of cold-induced thermogenesis / regulation of postsynapse organization / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / protein kinase activator activity / oligodendrocyte differentiation / cellular response to nutrient levels / positive regulation of TOR signaling / endomembrane system / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spliceosomal complex / GDP binding / postsynaptic density / lysosomal membrane / Golgi membrane / GTPase activity / dendrite / neuronal cell body / glutamatergic synapse / synapse / GTP binding / endoplasmic reticulum membrane / protein kinase binding / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / GTP-binding protein Rheb
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMazhab-Jafari, M.T. / Marshall, C.B. / Ho, J. / Ishiyama, N. / Stambolic, V. / Ikura, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-guided mutation of the conserved G3-box glycine in Rheb generates a constitutively activated regulator of mammalian target of rapamycin (mTOR).
Authors: Mazhab-Jafari, M.T. / Marshall, C.B. / Ho, J. / Ishiyama, N. / Stambolic, V. / Ikura, M.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein Rheb
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6928
Polymers38,4162
Non-polymers1,2766
Water2,252125
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7553
Polymers19,2081
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9375
Polymers19,2081
Non-polymers7294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.557, 70.248, 79.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GTP-binding protein Rheb / Ras homolog enriched in brain


Mass: 19207.955 Da / Num. of mol.: 2 / Fragment: UNP residues 1-169 / Mutation: G63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rheb / Production host: Escherichia coli (E. coli) / References: UniProt: Q921J2

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Non-polymers , 5 types, 131 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl [pH 8.5], 200 mM sodium acetate trihydrate, and 30% w/v Polyethylene Glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13176 / % possible obs: 100 % / Observed criterion σ(I): 3
Reflection shellResolution: 2.4→2.44 Å / % possible all: 100

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Processing

Software
NameClassification
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.9 Å /
RfactorNum. reflection
Rfree0.243 -
Rwork0.195 -
obs-12371
Refinement stepCycle: LAST / Resolution: 2.4→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 78 125 2855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d0.008
X-RAY DIFFRACTIONf_bond_d1.11

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