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- PDB-5yxh: Structure of Rheb-GDP -

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Basic information

Entry
Database: PDB / ID: 5yxh
TitleStructure of Rheb-GDP
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / GTPase / mTORC1 signaling / Rheb
Function / homology
Function and homology information


regulation of type B pancreatic cell development / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / Amino acids regulate mTORC1 / negative regulation of cold-induced thermogenesis / small GTPase-mediated signal transduction / Macroautophagy / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation ...regulation of type B pancreatic cell development / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / Amino acids regulate mTORC1 / negative regulation of cold-induced thermogenesis / small GTPase-mediated signal transduction / Macroautophagy / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / protein kinase activator activity / positive regulation of TOR signaling / regulation of macroautophagy / cellular response to nutrient levels / positive regulation of TORC1 signaling / endomembrane system / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / TP53 Regulates Metabolic Genes / spliceosomal complex / response to virus / GDP binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / regulation of cell cycle / postsynaptic density / Golgi membrane / lysosomal membrane / GTPase activity / endoplasmic reticulum membrane / protein kinase binding / GTP binding / magnesium ion binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold ...Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMahoney, S.J.
CitationJournal: Nat Commun / Year: 2018
Title: A small molecule inhibitor of Rheb selectively targets mTORC1 signaling.
Authors: Mahoney, S.J. / Narayan, S. / Molz, L. / Berstler, L.A. / Kang, S.A. / Vlasuk, G.P. / Saiah, E.
History
DepositionDec 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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
C: GTP-binding protein Rheb
D: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,97412
Polymers77,1044
Non-polymers1,8708
Water2,648147
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7433
Polymers19,2761
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)19,7433
Polymers19,2761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7433
Polymers19,2761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7433
Polymers19,2761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.166, 58.963, 64.345
Angle α, β, γ (deg.)110.53, 90.03, 108.16
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 19275.967 Da / Num. of mol.: 4
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
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.04→59.8 Å / Num. obs: 37982 / % possible obs: 91.5 % / Redundancy: 2 % / Net I/σ(I): 7.9
Reflection shellResolution: 2.04→2.09 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTQ

1xtq


Resolution: 2.04→59.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.541 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.247 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29862 1807 4.8 %RANDOM
Rwork0.24382 ---
obs0.24636 36174 91.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.78 Å20.01 Å2
2--1.54 Å2-0.22 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 2.04→59.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 116 147 5424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195380
X-RAY DIFFRACTIONr_bond_other_d0.0010.025167
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9887241
X-RAY DIFFRACTIONr_angle_other_deg0.729311901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6725.256234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49215987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2991520
X-RAY DIFFRACTIONr_chiral_restr0.060.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021167
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7384.0252595
X-RAY DIFFRACTIONr_mcbond_other1.7384.0252594
X-RAY DIFFRACTIONr_mcangle_it3.1066.0133228
X-RAY DIFFRACTIONr_mcangle_other3.1066.0133229
X-RAY DIFFRACTIONr_scbond_it1.2784.1772785
X-RAY DIFFRACTIONr_scbond_other1.2674.1812760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2486.2224001
X-RAY DIFFRACTIONr_long_range_B_refined5.18931.516037
X-RAY DIFFRACTIONr_long_range_B_other5.16731.4916010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 125 -
Rwork0.338 2577 -
obs--86.3 %

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