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

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Basic information

Entry
Database: PDB / ID: 5wbj
TitleCrystal structure of the arabidopsis thaliana Raptor in complex with the TOS peptide of human 4EBP1
Components
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • Regulatory-associated protein of TOR 1
KeywordsPROTEIN BINDING / Raptor / TOS
Function / homology
Function and homology information


maintenance of shoot apical meristem identity / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / TORC1 complex / TORC1 signaling / embryo development ending in seed dormancy / Cul4-RING E3 ubiquitin ligase complex / mTORC1-mediated signalling / TOR signaling / translation repressor activity ...maintenance of shoot apical meristem identity / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / TORC1 complex / TORC1 signaling / embryo development ending in seed dormancy / Cul4-RING E3 ubiquitin ligase complex / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / cellular response to starvation / negative regulation of autophagy / positive regulation of mitotic cell cycle / cellular response to amino acid stimulus / kinase binding / G1/S transition of mitotic cell cycle / protein-macromolecule adaptor activity / positive regulation of cell growth / negative regulation of translation / nucleus / cytoplasm / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E-binding protein 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 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

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Assembly

Deposited unit
A: Regulatory-associated protein of TOR 1
T: Eukaryotic translation initiation factor 4E-binding protein 1


Theoretical massNumber of molelcules
Total (without water)144,1542
Polymers144,1542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area45470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.100, 113.100, 153.500
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 Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


Mass: 2298.424 Da / Num. of mol.: 1 / Fragment: residues 99-118 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541

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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: 0.4 °
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→80 Å / Num. obs: 31652 / % possible obs: 98.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Χ2: 0.424 / Net I/σ(I): 5.3 / Num. measured all: 196625
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.117.20.8311831180.8010.3070.8620.40999.6
3.11-3.237.10.49931560.8950.1940.5380.41899.7
3.23-3.386.80.33631130.9450.1330.3640.41699.2
3.38-3.566.30.21331650.9750.0880.2320.41499.2
3.56-3.786.90.14431440.990.0560.1560.42199.3
3.78-4.076.50.09931630.9950.040.1070.43199.2
4.07-4.485.80.06531420.9970.0280.0710.43298.6
4.48-5.135.60.04731630.9980.0210.0520.44198.2
5.13-6.465.60.04831960.9980.0210.0530.43798.4
6.46-804.50.02832920.9990.0150.0330.43196.1

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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→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 54.688 / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26982 1403 4.8 %RANDOM
Rwork0.21528 ---
obs0.2179 27720 91.67 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.215 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å2-0 Å2-0 Å2
2---2.65 Å20 Å2
3---5.28 Å2
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8379 0 0 0 8379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198571
X-RAY DIFFRACTIONr_bond_other_d0.0020.028039
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9611641
X-RAY DIFFRACTIONr_angle_other_deg0.967318629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76851058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59523.737372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.945151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9721555
X-RAY DIFFRACTIONr_chiral_restr0.0780.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219432
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021747
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_it3.5693.544256
X-RAY DIFFRACTIONr_mcbond_other3.5683.544255
X-RAY DIFFRACTIONr_mcangle_it6.0197.0785306
X-RAY DIFFRACTIONr_mcangle_other6.0197.0785307
X-RAY DIFFRACTIONr_scbond_it3.3813.6524315
X-RAY DIFFRACTIONr_scbond_other3.383.6524316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8737.2296336
X-RAY DIFFRACTIONr_long_range_B_refined9.76581.239430
X-RAY DIFFRACTIONr_long_range_B_other9.76481.2359431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 83 -
Rwork0.371 1687 -
obs--77.84 %
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)
13.86480.1625-1.08082.8253-0.28793.2969-0.248-0.4467-0.31190.15960.0755-0.01880.1238-0.00160.17250.15420.04590.06970.1907-0.03630.0884-42.415-65.15638.369
25.7349-3.1671-1.6886.28841.27053.50250.19950.3308-0.2211-0.4212-0.2478-0.36120.26790.08530.04830.2633-0.01350.0970.1034-0.02790.0853-29.136-61.25219.698
33.67551.81070.28786.94571.98253.3681-0.1470.13930.1069-0.3183-0.1651-0.0646-0.0897-0.06950.3120.31780.03710.12620.07550.07820.2229-23.528-39.80918.534
46.15391.16941.82246.276-0.54654.6082-0.08630.018-0.2855-0.03-0.0542-0.39410.49680.40880.14060.24260.07890.05460.06440.08980.2597-13.599-23.86726.838
53.5907-2.2063-1.36445.3117-0.26233.633-0.1049-0.56770.25540.44440.1192-0.475-0.10180.2337-0.01440.1747-0.0337-0.01660.1590.05990.1992-14.979-2.72831.411
61.6982-0.03250.33282.8751-1.18184.10530.00710.5216-0.1356-0.41760.15430.27740.3065-0.7989-0.16140.0686-0.0378-0.02970.44910.04240.0845-28.36515.3980.616
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 DIFFRACTION3T111 - 118
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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