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- PDB-5wbk: Crystal structure of the arabidopsis thaliana Raptor in complex w... -

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Basic information

Entry
Database: PDB / ID: 5wbk
TitleCrystal structure of the arabidopsis thaliana Raptor in complex with the TOS peptide of human S6K1
Components
  • Regulatory-associated protein of TOR 1
  • Ribosomal protein S6 kinase beta-1
KeywordsPROTEIN BINDING / Raptor / TOS
Function / homology
Function and homology information


maintenance of shoot apical meristem identity / long-chain fatty acid import into cell / TORC1 complex / negative regulation of TORC2 signaling / embryo development ending in seed dormancy / cellular response to nutrient / TORC1 signaling / Cul4-RING E3 ubiquitin ligase complex / phosphatidylinositol-mediated signaling / germ cell development ...maintenance of shoot apical meristem identity / long-chain fatty acid import into cell / TORC1 complex / negative regulation of TORC2 signaling / embryo development ending in seed dormancy / cellular response to nutrient / TORC1 signaling / Cul4-RING E3 ubiquitin ligase complex / phosphatidylinositol-mediated signaling / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / behavioral fear response / positive regulation of TORC1 signaling / cellular response to dexamethasone stimulus / protein serine/threonine/tyrosine kinase activity / negative regulation of autophagy / negative regulation of insulin receptor signaling pathway / positive regulation of mitotic cell cycle / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / cellular response to growth factor stimulus / cellular response to type II interferon / kinase binding / cellular response to insulin stimulus / peptidyl-serine phosphorylation / mitochondrial outer membrane / neuron projection / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / glutamatergic synapse / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...Ribosomal protein S6 kinase / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / Trp-Asp (WD) repeats circular profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ribosomal protein S6 kinase beta-1 / Regulatory-associated protein of TOR 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsPavletich, N.P. / Jiang, X.
CitationJournal: Nature / Year: 2017
Title: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40.
Authors: Haijuan Yang / Xiaolu Jiang / Buren Li / Hyo J Yang / Meredith Miller / Angela Yang / Ankita Dhar / Nikola P Pavletich /
Abstract: The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the ...The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB-mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR-TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12-rapamycin-binding (FRB) domain-substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR-PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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: Regulatory-associated protein of TOR 1
T: Ribosomal protein S6 kinase beta-1


Theoretical massNumber of molelcules
Total (without water)143,4202
Polymers143,4202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area45530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.100, 113.100, 152.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regulatory-associated protein of TOR 1 / Protein RAPTOR 1 / Protein RAPTOR 1B / AtRaptor1b


Mass: 141855.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAPTOR1, RAPTOR1B, At3g08850, T16O11.22
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q93YQ1
#2: Protein/peptide Ribosomal protein S6 kinase beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / p70-S6K 1 / Ribosomal protein S6 kinase I / ...S6K1 / 70 kDa ribosomal protein S6 kinase 1 / p70-S6K 1 / Ribosomal protein S6 kinase I / Serine/threonine-protein kinase 14A / p70 ribosomal S6 kinase alpha / p70 S6KA


Mass: 1564.670 Da / Num. of mol.: 1 / Fragment: residues 24-37 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P23443, non-specific serine/threonine protein kinase

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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: 2.69 Å3/Da / Density % sol: 54.2 % / Mosaicity: 0.818 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→80 Å / Num. obs: 27998 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Χ2: 0.408 / Net I/σ(I): 5.3 / Num. measured all: 182755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.216.90.819275927590.8460.3310.8850.39599.4
3.21-3.346.40.53227290.9110.2230.5790.498.9
3.34-3.497.20.37927750.9530.150.4090.40199.8
3.49-3.6870.24327930.980.0980.2630.40499.8
3.68-3.916.80.16427680.990.0670.1770.40499.5
3.91-4.216.30.10527760.9950.0450.1150.41298.8
4.21-4.636.70.06927910.9980.0290.0750.41399.5
4.63-5.36.30.05528010.9980.0240.060.41899.2
5.3-6.686.30.05428380.9980.0230.0590.42399.1
6.68-805.50.02729680.9990.0130.030.40998.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WBI

5wbi


Resolution: 3.11→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 55.101 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.477 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25463 1057 4 %RANDOM
Rwork0.20917 ---
obs0.21101 25050 92.03 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.936 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0 Å2
2---4.61 Å20 Å2
3---4.47 Å2
Refinement stepCycle: 1 / Resolution: 3.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8332 0 0 0 8332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198522
X-RAY DIFFRACTIONr_bond_other_d0.0020.027994
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9611575
X-RAY DIFFRACTIONr_angle_other_deg0.964318516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38151052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43823.703370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.194151437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3691555
X-RAY DIFFRACTIONr_chiral_restr0.0760.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021742
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6853.2664235
X-RAY DIFFRACTIONr_mcbond_other2.6853.2664234
X-RAY DIFFRACTIONr_mcangle_it4.6486.5295278
X-RAY DIFFRACTIONr_mcangle_other4.6476.5295279
X-RAY DIFFRACTIONr_scbond_it2.5243.3564287
X-RAY DIFFRACTIONr_scbond_other2.5233.3574288
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4616.6526298
X-RAY DIFFRACTIONr_long_range_B_refined7.71574.7089345
X-RAY DIFFRACTIONr_long_range_B_other7.71574.7139346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.114→3.193 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 62 -
Rwork0.342 1414 -
obs--72.71 %
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)
14.01320.0224-1.32092.1105-0.1233.3098-0.1914-0.3087-0.26330.27020.0919-0.06590.12840.10320.09960.24450.04410.12240.2265-0.06180.2724-42.204-64.63438.293
26.1938-3.3069-2.10116.12510.89973.73740.26760.379-0.0692-0.4201-0.1975-0.58020.18260.0519-0.07020.31880.00970.1320.1797-0.01260.2899-28.918-61.10519.486
33.61612.12331.1666.70562.56243.9112-0.15220.1419-0.0903-0.0532-0.1329-0.1610.1337-0.16080.28510.40340.05520.17110.18520.07780.3958-23.263-39.60418.434
45.96291.14892.06766.31130.36413.817-0.0380.1111-0.5590.1896-0.0363-0.31810.25570.31240.07420.27010.08810.06180.12350.09220.3382-13.406-23.74127.153
54.4434-2.8515-1.81956.0885-0.29784.4015-0.0232-0.61860.20260.54440.1322-0.5458-0.16840.1941-0.10910.2289-0.04620.02580.2030.13170.2926-14.809-2.53231.739
63.17820.11130.25663.4977-1.23684.2136-0.05110.5931-0.1752-0.45260.20170.31370.3682-0.9088-0.15050.0731-0.0628-0.02840.5250.09620.0985-27.9115.4180.618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A106 - 303
2X-RAY DIFFRACTION1A372 - 404
3X-RAY DIFFRACTION2A100 - 105
4X-RAY DIFFRACTION2A304 - 371
5X-RAY DIFFRACTION2A405 - 437
6X-RAY DIFFRACTION3A438 - 534
7X-RAY DIFFRACTION3A95 - 99
8X-RAY DIFFRACTION3T2 - 9
9X-RAY DIFFRACTION4A90 - 94
10X-RAY DIFFRACTION4A535 - 599
11X-RAY DIFFRACTION4A966 - 978
12X-RAY DIFFRACTION5A75 - 89
13X-RAY DIFFRACTION5A609 - 865
14X-RAY DIFFRACTION5A957 - 965
15X-RAY DIFFRACTION6A985 - 1339
16X-RAY DIFFRACTION6A61 - 74

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