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- PDB-6bsx: CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND 1 AT 1.65A RES... -

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Basic information

Entry
Database: PDB / ID: 6bsx
TitleCRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND 1 AT 1.65A RESOLUTION
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / mTORC1 G-protein
Function / homology
Function and homology information


regulation of type B pancreatic cell development / Amino acids regulate mTORC1 / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / Macroautophagy / protein kinase activator activity / oligodendrocyte differentiation ...regulation of type B pancreatic cell development / Amino acids regulate mTORC1 / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / Macroautophagy / protein kinase activator activity / oligodendrocyte differentiation / mTORC1-mediated signalling / positive regulation of TOR signaling / endomembrane system / regulation of macroautophagy / cellular response to nutrient levels / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / TP53 Regulates Metabolic Genes / spliceosomal complex / GDP binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / postsynaptic density / regulation of cell cycle / lysosomal membrane / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / 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 / Rossmann fold ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (5,6-dimethyl-1H-benzimidazol-2-yl)methanol / GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 4, 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_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 / _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

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)84,00424
Polymers80,9444
Non-polymers3,05920
Water9,800544
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0016
Polymers20,2361
Non-polymers7655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0016
Polymers20,2361
Non-polymers7655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0016
Polymers20,2361
Non-polymers7655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0016
Polymers20,2361
Non-polymers7655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.370, 49.720, 70.970
Angle α, β, γ (deg.)89.990, 77.700, 89.870
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 20236.045 Da / Num. of mol.: 4 / Fragment: RHEB VCID 10367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHEB, RHEB2 / Plasmid: PEMB32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15382

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Non-polymers , 6 types, 564 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-E7S / (5,6-dimethyl-1H-benzimidazol-2-yl)methanol


Mass: 176.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.8
Details: 28% PEG4000, 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, PH 8.8, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 73559 / % possible obs: 92.7 % / Redundancy: 2 % / Biso Wilson estimate: 16.05 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.09
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.5 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIXDEV_1883refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTQ

1xtq


Resolution: 1.65→29.264 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.01
RfactorNum. reflection% reflection
Rfree0.2438 1989 2.71 %
Rwork0.1973 --
obs0.1986 73526 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65 Å2 / Biso mean: 22.5096 Å2 / Biso min: 7.99 Å2
Refinement stepCycle: final / Resolution: 1.65→29.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5235 0 200 544 5979
Biso mean--26.59 31.05 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165602
X-RAY DIFFRACTIONf_angle_d1.5087612
X-RAY DIFFRACTIONf_chiral_restr0.066881
X-RAY DIFFRACTIONf_plane_restr0.008932
X-RAY DIFFRACTIONf_dihedral_angle_d14.5142003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69130.31421410.27525107524893
1.6913-1.7370.3131420.255151529393
1.737-1.78810.28911420.24085175531794
1.7881-1.84580.30751430.22095188533193
1.8458-1.91180.27431470.20645124527194
1.9118-1.98830.21541410.20115134527593
1.9883-2.07880.2581430.19955111525493
2.0788-2.18830.26351480.1925122527093
2.1883-2.32540.24871420.18525093523593
2.3254-2.50480.28061440.18865115525993
2.5048-2.75670.26421430.20495101524492
2.7567-3.15520.24281380.20165077521592
3.1552-3.97370.20011400.17325025516591
3.9737-29.26830.20971350.18965014514991
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0639-0.002-0.13610.0309-0.00610.01610.00630.067-0.038-0.0021-0.0612-0.0701-0.0055-0.0129-0.00380.15280.01190.0260.1177-0.01450.195-21.3272-20.539-49.3541
20.16180.10830.05130.12980.09460.0949-0.0494-0.18490.04360.06880.0355-0.1025-0.00420.02860.00030.12410.00110.00080.1462-0.0010.1307-23.1857-8.9983-35.9425
30.0196-0.02080.03770.0425-0.0620.02880.064-0.0159-0.10380.1432-0.0354-0.0754-0.0329-0.0433-00.1531-0.00090.01140.15470.01150.2484-21.3849-21.6347-41.5277
40.0949-0.0175-0.01840.00880.02710.01290.0553-0.1064-0.32650.2237-0.0588-0.1114-0.0005-0.07970.00010.1357-0.0033-0.00430.11880.01230.2596-22.4879-23.5213-46.0589
50.07570.0162-0.0760.0062-0.01770.08440.12040.39370.2867-0.07860.14710.0372-0.60010.0190.06850.26730.1140.1537-0.8602-0.00910.4209-20.3021.0921-49.9813
60.03330.00030.15840.0632-0.03570.24020.1296-0.0440.2598-0.14590.0083-0.35490.04820.09370.00960.14070.03030.06620.10780.01140.1962-23.677-8.4281-50.2743
70.43340.16990.0220.1745-0.06910.37870.07060.15240.3963-0.2386-0.14160.088-0.26730.0294-0.09390.1775-0.00660.03560.1470.07920.1105-27.986-1.0601-53.6468
80.0679-0.02670.04360.018-0.01570.0205-0.08640.00810.052-0.12210.02150.17460.1739-0.09160.00010.1973-0.0151-0.00370.12960.01230.145-29.1816-11.8143-53.5041
90.1446-0.26780.02860.3137-0.09290.0468-0.06360.0298-0.0449-0.0090.02320.1431-0.02970.00060.0020.09840.01050.00890.15130.00560.1707-40.0495-4.2706-44.7975
100.30690.15640.10430.1861-0.10380.1062-0.1019-0.0513-0.1092-0.03550.06450.07750.0026-0.0509-0.01050.1204-0.00890.01840.10690.02830.1616-33.2422-17.1766-45.9098
110.46230.10260.16070.0658-0.02440.18510.00440.1023-0.1046-0.05630.02660.195-0.0346-0.0109-0.00390.1269-0.00840.01570.12060.00280.1477-7.190310.3545-48.6424
120.79650.3286-0.18390.371-0.20090.21260.06020.06990.01590.024-0.05870.2047-0.0062-0.0032-0.01720.102-0.00780.00990.1002-0.00720.1392-8.675612.4003-46.6345
130.22530.0337-0.18540.0250.0750.18190.2169-0.13250.3310.2004-0.0210.1379-0.22120.02850.01630.1698-0.00860.02940.1361-0.0390.1129-2.507824.1058-37.9457
140.34060.29830.09040.29050.20820.1519-0.0084-0.03430.03090.04520.0231-0.1211-0.01560.07920.02740.1113-0.01060.00110.1415-0.00830.15016.155718.3648-44.0192
150.3743-0.20370.06930.1659-0.050.0167-0.09450.0055-0.1792-0.02160.0857-0.10430.02480.07240.00870.15290.00630.01130.139-0.03240.15552.37077.5389-45.2716
160.0041-0.01710.04890.05430.02160.02420.04260.04250.1144-0.1207-0.01510.11070.0606-0.06860.01130.12020.0085-0.03660.10250.0480.3071-26.475121.5754-14.7409
170.16650.03450.01580.0442-0.09690.1756-0.101-0.22250.1053-0.04210.07160.15470.0295-0.03710.01190.1093-0.00390.01170.1535-0.02670.1923-24.74459.4516-1.6188
180.2649-0.04630.03220.0456-0.2010.37830.0530.01130.0405-0.0066-0.00510.39560.09360.01690.00520.13650.0104-0.03260.12080.00620.3051-26.377816.9271-11.2055
190.1210.0129-0.11740.27880.30570.47450.07340.0166-0.0719-0.1094-0.05730.2084-0.054-0.0889-0.00020.13290.0177-0.04660.1219-0.00760.1738-21.19656.9267-17.307
200.49050.28820.03590.38080.10050.3935-0.0186-0.06650.21540.015-0.0249-0.04930.04290.1069-0.02540.10790.0043-0.01070.1232-0.01350.1364-11.624112.4364-10.5941
210.33660.1895-0.1460.1740.10530.210.00640.17390.3372-0.0939-0.0714-0.3060.12560.1835-0.01250.0858-0.0309-0.02470.10390.01430.26838.6622-8.8408-13.8314
220.0440.019-0.05430.0274-0.0480.01230.01210.29360.1251-0.0664-0.0456-0.3665-0.05280.1790.00010.14230.01370.04770.21670.00110.215212.0073-16.5262-22.7669
230.36470.06330.08390.02090.12230.3530.02510.01480.0260.0326-0.0432-0.32560.0690.02240.01210.12250.0096-0.02470.1014-0.01010.30310.83-8.9007-10.7036
240.16840.0503-0.19390.26840.00550.22160.2220.2676-0.13860.1829-0.0911-0.6610.1350.1344-0.00920.1178-0.0436-0.08960.04610.01550.24048.6287-15.3208-6.3455
250.23580.00740.16950.0289-0.08090.15610.1109-0.1515-0.38080.1647-0.0007-0.24480.25750.0953-0.0290.13030.0037-0.05730.15220.04180.13194.2892-22.8232-3.102
260.0688-0.0348-0.0420.0130.04430.03320.07110.06780.18340.0335-0.01790.073-0.1269-0.04970.01860.1252-0.03420.02460.1338-0.04610.15742.1474-12.9353-4.6756
270.0455-0.0241-0.0070.02170.03910.0565-0.09590.1972-0.0982-0.0030.10150.11640.0908-0.1216-0.01320.1322-0.0119-0.00970.1572-0.00370.0729-7.5457-21.6595-19.9717
280.2209-0.19140.01750.24330.02720.06630.0043-0.02770.17820.00830.0340.08730.0003-0.10010.00010.1364-0.0113-0.00370.13820.00410.1222-5.9268-15.2282-8.7833
290.0609-0.0881-0.01010.1379-0.00090.0280.013-0.01580.3511-0.0206-0.0106-0.0787-0.2663-0.22940.00530.16190.0048-0.03870.14710.02570.30380.4736-3.6125-9.2286
300.12780.0342-0.06380.0222-0.00730.03620.0787-0.2169-0.0202-0.0479-0.00560.1862-0.0466-0.0504-0.00020.1922-0.0084-0.00750.2325-0.0410.0762-27.5201-4.5927-34.8711
315.9718-0.03094.33176.7154.08596.442-0.1197-0.0204-0.00180.06220.0339-0.1082-0.0218-0.16130.16820.2198-0.0820.09190.48630.1770.3219-17.4262-6.6778-49.8919
320.05480.0427-0.0740.0366-0.06270.0870.0230.36410.1393-0.00170.0636-0.01490.04450.15180.10880.2256-0.0151-0.00780.2140.02720.0674-3.139620.2398-56.5241
337.84631.22212.93797.8883-4.22098.4151-0.2370.02310.0312-0.22330.07830.1497-0.25460.26580.23830.32840.1950.05110.657-0.03750.5765-13.235318.1964-41.4813
340.08360.01970.05050.00540.00910.0250.1382-0.2652-0.0215-0.11120.03870.1085-0.02260.0715-0.00050.1834-0.01270.03730.18850.02340.1183-20.38495.6346-0.2501
355.76211.09590.46193.05812.8372.6947-0.3488-0.2028-0.1890.43250.01490.39270.30830.39270.26120.395-0.2769-0.11650.83420.13240.6103-30.28677.4854-15.3792
360.0917-0.02360.04220.0075-0.01590.01710.10740.355-0.05260.0363-0.0419-0.0512-0.1471-0.08070.00010.1779-0.00690.02980.1903-0.01530.11494.7711-19.2182-21.8064
372.7521-2.6228-2.71822.61722.52072.7273-0.26930.0482-0.0265-0.28510.109-0.23480.3158-0.33480.1670.20730.0195-0.04450.7455-0.05340.350214.6195-17.7274-6.7038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth seq-ID
1X-RAY DIFFRACTION10
2X-RAY DIFFRACTION20
3X-RAY DIFFRACTION30
4X-RAY DIFFRACTION40
5X-RAY DIFFRACTION50
6X-RAY DIFFRACTION60
7X-RAY DIFFRACTION70
8X-RAY DIFFRACTION80
9X-RAY DIFFRACTION90
10X-RAY DIFFRACTION100
11X-RAY DIFFRACTION110
12X-RAY DIFFRACTION120
13X-RAY DIFFRACTION130
14X-RAY DIFFRACTION140
15X-RAY DIFFRACTION150
16X-RAY DIFFRACTION160
17X-RAY DIFFRACTION170
18X-RAY DIFFRACTION180
19X-RAY DIFFRACTION190
20X-RAY DIFFRACTION200
21X-RAY DIFFRACTION210
22X-RAY DIFFRACTION220
23X-RAY DIFFRACTION230
24X-RAY DIFFRACTION240
25X-RAY DIFFRACTION250
26X-RAY DIFFRACTION260
27X-RAY DIFFRACTION270
28X-RAY DIFFRACTION280
29X-RAY DIFFRACTION290
30X-RAY DIFFRACTION300
31X-RAY DIFFRACTION310
32X-RAY DIFFRACTION320
33X-RAY DIFFRACTION330
34X-RAY DIFFRACTION340
35X-RAY DIFFRACTION350
36X-RAY DIFFRACTION360
37X-RAY DIFFRACTION370

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