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- PDB-7bta: Crystal structure of Rheb D60K mutant bound to GDP -

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Basic information

Entry
Database: PDB / ID: 7bta
TitleCrystal structure of Rheb D60K mutant bound to GDP
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / mTORC1 / small GTPase / Rheb
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 / regulation of macroautophagy / cellular response to nutrient levels / endomembrane system / 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 / Golgi membrane / lysosomal 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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, C. / Zhang, T. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870722 China
CitationJournal: J Mol Cell Biol / Year: 2020
Title: Molecular basis for the functions of dominantly active Y35N and inactive D60K Rheb mutants in mTORC1 signaling.
Authors: Zhang, C. / Liu, Y. / Zhang, Y. / Wang, X. / Zhang, T. / Ding, J.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4026
Polymers40,3262
Non-polymers1,0764
Water21612
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7013
Polymers20,1631
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area8100 Å2
MethodPISA
2
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7013
Polymers20,1631
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-6 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.860, 47.800, 61.070
Angle α, β, γ (deg.)90.000, 112.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20163.057 Da / Num. of mol.: 2 / Fragment: GTPase domain / Mutation: D60K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHEB, RHEB2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15382
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.82 Å3/Da / Density % sol: 32.3 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 8 / Details: 0.2 M NaH2PO4: 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→31.852 Å / Num. obs: 9007 / % possible obs: 97.8 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 679 / CC1/2: 0.881

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTQ

1xtq


Resolution: 2.6→31.852 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.2559 423 4.72 %
Rwork0.1905 --
obs0.1936 8967 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 51.4272 Å2 / Biso min: 19.63 Å2
Refinement stepCycle: final / Resolution: 2.6→31.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 66 12 2489
Biso mean--46.6 36.82 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092514
X-RAY DIFFRACTIONf_angle_d1.1653398
X-RAY DIFFRACTIONf_chiral_restr0.059399
X-RAY DIFFRACTIONf_plane_restr0.006408
X-RAY DIFFRACTIONf_dihedral_angle_d18.291496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6005-2.97650.33541370.2327278497
2.9765-3.74920.24731390.19862842100
3.7492-31.8520.24031470.1743291899
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)
13.739-1.8206-0.22813.4499-0.44133.7992-0.1237-0.0196-0.1913-0.03990.27110.26420.0064-0.16890.08130.2826-0.0611-0.03720.2030.02930.3843108.1341-9.734729.9765
21.2951-1.2580.55711.6858-1.0710.855-0.7853-0.4493-0.63841.56780.7631.30980.3508-0.9484-0.02460.4626-0.02640.2150.7831-0.07790.9513105.0207-12.341239.5828
35.4137-1.5539-0.7444.9316-0.44544.48750.23960.07360.47020.4579-0.1680.2292-0.5987-0.6053-0.02360.3798-0.0167-0.08230.24040.01140.3716105.8428-0.253928.338
41.10990.75140.39167.3811-0.76183.3432-0.15661.2369-1.1282-1.58490.09691.52420.5647-0.86790.22150.7314-0.1926-0.09420.6788-0.14821.2388104.6954-23.879822.6943
51.55191.0661-0.8962.65710.87271.87680.14290.1179-1.5248-1.05710.78252.10910.7615-1.85820.11610.4823-0.0375-0.0981-0.094-0.07310.6906109.4999-14.311323.4257
64.6045-1.9563-0.18095.7799-0.47624.61110.07140.4861-0.4807-0.7046-0.25250.32390.3721-0.25190.05890.3436-0.0389-0.0710.2441-0.07770.449113.6305-18.0819.2882
73.3812-2.0512-0.48264.12140.28983.1429-0.118-0.06210.29870.08820.0462-0.2321-0.08780.40910.1520.2626-0.0416-0.05520.19260.00830.3463120.6656-11.083928.507
84.22472.2079-0.24993.1330.95133.7914-0.02370.29970.2166-0.7080.04570.4098-0.6213-0.55610.07260.45890.0832-0.06170.24340.01840.3311102.6383-36.234743.3461
94.57061.41290.152.69071.49733.7020.0340.5262-0.0383-0.52230.2959-0.0073-0.1405-0.39480.01360.45720.0248-0.02340.3079-0.03350.4891102.5853-44.228541.2022
104.73181.66140.46064.96271.95433.4567-0.1297-0.67410.9569-0.5237-0.22491.1419-0.9463-0.59250.17690.52380.1801-0.07510.3368-0.08070.467599.4702-28.383152.7304
113.79852.02060.09643.90461.45553.15260.2509-0.2418-0.1911-0.2397-0.1778-0.0525-0.19450.005-0.04040.39710.0381-0.02360.1986-0.00150.3513109.8255-35.019353.4722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 27 )A4 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 40 )A28 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 60 )A41 - 60
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 71 )A61 - 71
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 89 )A72 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 119 )A90 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 170 )A120 - 170
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 27 )B4 - 27
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 60 )B28 - 60
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 113 )B61 - 113
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 170 )B114 - 170

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