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- PDB-3sea: Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms -

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Basic information

Entry
Database: PDB / ID: 3sea
TitleStructure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms
ComponentsGTP-binding protein Rheb
KeywordsHYDROLASE / globular
Function / homology
Function and homology information


regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / protein kinase activator activity / oligodendrocyte differentiation ...regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / protein kinase activator activity / oligodendrocyte differentiation / mTORC1-mediated signalling / cellular response to nutrient levels / positive regulation of TOR signaling / regulation of macroautophagy / endomembrane system / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / spliceosomal complex / TP53 Regulates Metabolic Genes / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GDP binding / postsynaptic density / regulation of cell cycle / lysosomal membrane / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / membrane / 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'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMazhab-Jafari, M.T. / Marshall, C.B. / Ishiyama, N. / Vuk, S. / Ikura, M.
CitationJournal: Structure / Year: 2012
Title: An Autoinhibited Noncanonical Mechanism of GTP Hydrolysis by Rheb Maintains mTORC1 Homeostasis.
Authors: Mazhab-Jafari, M.T. / Marshall, C.B. / Ishiyama, N. / Ho, J. / Di Palma, V. / Stambolic, V. / Ikura, M.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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

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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)38,5887
Polymers37,5152
Non-polymers1,0735
Water4,540252
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2253
Polymers18,7571
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3634
Polymers18,7571
Non-polymers6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: GTP-binding protein Rheb
hetero molecules

B: GTP-binding protein Rheb
hetero molecules

A: GTP-binding protein Rheb
hetero molecules

A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,17614
Polymers75,0304
Non-polymers2,14610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
crystal symmetry operation4_444-x-1,-y-1/2,z-1/21
Buried area8580 Å2
ΔGint-98 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.247, 69.873, 79.195
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: 18757.406 Da / Num. of mol.: 2 / Fragment: G-domain / Mutation: Y35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHEB, RHEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15382

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*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.: 252 / 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: 41.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris hydrochloride, 200 mM Sodium acetate trihydrate, 30% w/v Polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21742 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 20.711
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 4.597 / Rsym value: 0.412 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XTR

1xtr


Resolution: 2→26.919 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 1961 9.02 %
Rwork0.1618 --
obs0.1665 21742 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.249 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1797 Å20 Å2-0 Å2
2---0.3176 Å20 Å2
3----5.8621 Å2
Refinement stepCycle: LAST / Resolution: 2→26.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 66 252 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072904
X-RAY DIFFRACTIONf_angle_d1.1413963
X-RAY DIFFRACTIONf_dihedral_angle_d16.5991121
X-RAY DIFFRACTIONf_chiral_restr0.075456
X-RAY DIFFRACTIONf_plane_restr0.004495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06970.24921830.16841876X-RAY DIFFRACTION95
2.0697-2.15260.23911910.1631907X-RAY DIFFRACTION97
2.1526-2.25050.25851900.16281947X-RAY DIFFRACTION98
2.2505-2.36910.22421910.16511932X-RAY DIFFRACTION97
2.3691-2.51740.23571980.15891965X-RAY DIFFRACTION98
2.5174-2.71160.2511960.16661966X-RAY DIFFRACTION99
2.7116-2.98420.21991990.172007X-RAY DIFFRACTION100
2.9842-3.41530.22951980.17242007X-RAY DIFFRACTION100
3.4153-4.30.18622030.14772040X-RAY DIFFRACTION100
4.3-26.92160.17732120.16022134X-RAY DIFFRACTION99

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