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- PDB-7btd: Crystal structure of Rheb Y35N mutant bound to GppNHp -

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Basic information

Entry
Database: PDB / ID: 7btd
TitleCrystal structure of Rheb Y35N mutant bound to GppNHp
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / mTORC1 / small GTPase / Rheb
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 / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / 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 / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / 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 / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionApr 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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.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 1.2Nov 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

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Assembly

Deposited unit
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6463
Polymers20,1001
Non-polymers5472
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-14 kcal/mol
Surface area8420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.637, 102.962, 47.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20099.895 Da / Num. of mol.: 1 / Fragment: GTPase domain / Mutation: Y35N
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.98 Å3/Da / Density % sol: 58.77 % / Mosaicity: 0.364 °
Crystal growTemperature: 290 K / Method: evaporation / pH: 7.5
Details: 0.2 M Ammonium acetate: 0.1 M HEPES, pH 7.5: 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50.01 Å / Num. obs: 16650 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.108 / Χ2: 0.784 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.076.30.54716220.90.2320.5960.52599.1
2.07-2.156.70.44216290.9240.1830.480.51399.6
2.15-2.257.10.35816460.9520.1440.3870.597100
2.25-2.377.60.29116500.9590.1130.3130.63999.9
2.37-2.527.50.21516540.9780.0840.2310.69899.9
2.52-2.717.20.17516510.9830.0690.1890.79100
2.71-2.997.10.13416630.9880.0540.1450.88399.9
2.99-3.427.50.09916730.9920.0380.1060.98100
3.42-4.316.90.07116860.9940.0290.0771.10899.7
4.31-5070.06117760.9960.0250.0661.02999.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTS

1xts


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.26 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.13 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 833 5 %RANDOM
Rwork0.1661 ---
obs0.168 15789 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.22 Å2 / Biso mean: 38.068 Å2 / Biso min: 20.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0 Å2
2--0.35 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 33 105 1478
Biso mean--30.46 46.52 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191395
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.991891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44625.4161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51815256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.415155
X-RAY DIFFRACTIONr_chiral_restr0.0670.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021006
X-RAY DIFFRACTIONr_rigid_bond_restr1.4131394
X-RAY DIFFRACTIONr_sphericity_free14.664554
X-RAY DIFFRACTIONr_sphericity_bonded16.12151424
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 60 -
Rwork0.216 1128 -
all-1188 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: -14.9459 Å / Origin y: -33.2213 Å / Origin z: 7.8789 Å
111213212223313233
T0.1139 Å20.0027 Å2-0.0014 Å2-0.1207 Å20.0016 Å2--0.0008 Å2
L0.0029 °20.0045 °2-0.0094 °2-0.0073 °2-0.0143 °2--0.0301 °2
S-0.0019 Å °-0.0036 Å °-0.0015 Å °-0.0092 Å °-0.0033 Å °-0.0021 Å °0.0042 Å °0.0124 Å °0.0052 Å °

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