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- PDB-6bt0: CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND NR1 -

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Basic information

Entry
Database: PDB / ID: 6bt0
TitleCRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND NR1
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / mTORC1 G-protein
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 / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / 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 / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Metabolic Genes / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spliceosomal complex / 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
Chem-E7V / GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns_shell / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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.value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _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
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)83,39313
Polymers80,9444
Non-polymers2,4489
Water32418
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7043
Polymers20,2361
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)21,2824
Polymers20,2361
Non-polymers1,0463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7043
Polymers20,2361
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)20,7043
Polymers20,2361
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.150, 60.140, 66.320
Angle α, β, γ (deg.)68.350, 90.010, 72.050
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: 20236.045 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) / Strain (production host): BL21(DE3) / References: UniProt: Q15382
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-E7V / 4-bromo-6-[(3,4-dichlorophenyl)sulfanyl]-1-{[4-(dimethylcarbamoyl)phenyl]methyl}-1H-indole-2-carboxylic acid


Mass: 578.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H19BrCl2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 19% PEG 1500, 0.1M Na acetate pH 5.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→46.37 Å / Num. obs: 18856 / % possible obs: 84.7 % / Redundancy: 1.989 % / Biso Wilson estimate: 37.612 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.312 / Rrim(I) all: 0.441 / Χ2: 0.938 / Net I/σ(I): 2.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obs% possible allRmerge(I) obsRrim(I) allCC1/2
1.78-1.831.9580.03273557.9
1.83-1.881.9450.43254955.51.5852.242
1.88-1.931.9610.74232652.41.1361.6070.574
1.93-1.991.993405593.90.102
1.99-2.061.9950.25402195.33.1214.414
2.06-2.131.9940.34387295.42.4593.478
2.13-2.211.9950.3371594.62.6563.756
2.21-2.31.9960.52233062.51.4512.0520.776
2.3-2.41.9950.67346195.41.2761.8040.221
2.4-2.521.9940.92333895.90.9481.3410.308
2.52-2.651.9941.283138960.7010.9910.434
2.65-2.811.9951.68297895.90.5580.7890.547
2.81-3.011.9942.61281195.60.3480.4920.759
3.01-3.251.9954.01261396.10.220.310.892
3.25-3.561.9946.04240396.60.1280.180.967
3.56-3.981.9958.49201589.30.0970.1370.974
3.98-4.61.99511.291944970.0620.0870.988
4.6-5.631.99311.31162897.40.0580.0810.989
5.63-7.961.99210.95127196.80.060.0850.992
7.96-46.371.98619.5969096.10.0310.0430.996

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTQ

1xtq


Resolution: 2.6→46.37 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.818 / SU B: 21.282 / SU ML: 0.443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.477
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3164 943 5 %RANDOM
Rwork0.2168 ---
obs0.2219 17913 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.51 Å2 / Biso mean: 36.907 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.7 Å20.17 Å2
2--1.37 Å20.55 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.6→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5349 0 150 18 5517
Biso mean--51.84 20.37 -
Num. residues----673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195594
X-RAY DIFFRACTIONr_bond_other_d0.0020.025376
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9947582
X-RAY DIFFRACTIONr_angle_other_deg0.991312384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3845669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5925.187241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6011520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021231
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 71 -
Rwork0.304 1335 -
all-1406 -
obs--96.17 %

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