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- PDB-2l0x: Solution structure of the 21 kDa GTPase RHEB bound to GDP -

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Basic information

Entry
Database: PDB / ID: 2l0x
TitleSolution structure of the 21 kDa GTPase RHEB bound to GDP
ComponentsGTP-binding protein Rheb
KeywordsHYDROLASE / GTPASE
Function / homology
Function and homology information


MTOR signalling / Regulation of PTEN gene transcription / mTORC1-mediated signalling / Energy dependent regulation of mTOR by LKB1-AMPK / Macroautophagy / TP53 Regulates Metabolic Genes / Amino acids regulate mTORC1 / regulation of type B pancreatic cell development / regulation of TOR signaling / regulation of postsynapse organization ...MTOR signalling / Regulation of PTEN gene transcription / mTORC1-mediated signalling / Energy dependent regulation of mTOR by LKB1-AMPK / Macroautophagy / TP53 Regulates Metabolic Genes / Amino acids regulate mTORC1 / regulation of type B pancreatic cell development / regulation of TOR signaling / regulation of postsynapse organization / negative regulation of cold-induced thermogenesis / small GTPase-mediated signal transduction / oligodendrocyte differentiation / regulation of neuronal synaptic plasticity / positive regulation of oligodendrocyte differentiation / protein kinase activator activity / positive regulation of TOR signaling / cellular response to nutrient levels / positive regulation of TORC1 signaling / endomembrane system / protein serine/threonine kinase activator activity / spliceosomal complex / GDP binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / postsynaptic density / Golgi membrane / lysosomal membrane / GTPase activity / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / protein kinase binding / GTP binding / glutamatergic synapse / magnesium ion binding / 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
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein Rheb
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsStoll, R. / Heumann, R. / Berghaus, C. / Kock, G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Ras homolog enriched in brain (Rheb) enhances apoptotic signaling.
Authors: Karassek, S. / Berghaus, C. / Schwarten, M. / Goemans, C.G. / Ohse, N. / Kock, G. / Jockers, K. / Neumann, S. / Gottfried, S. / Herrmann, C. / Heumann, R. / Stoll, R.
History
DepositionJul 19, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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.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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4003
Polymers18,9331
Non-polymers4682
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 18932.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rheb / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62639
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNHA

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Sample preparation

DetailsContents: 0.9-1.2 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: entity_1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.9-1.2
Sample conditionspH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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