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- PDB-7ped: DEPTOR DEP domain tandem (DEPt) -

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Basic information

Entry
Database: PDB / ID: 7ped
TitleDEPTOR DEP domain tandem (DEPt)
ComponentsDEP domain-containing mTOR-interacting protein
KeywordsSIGNALING PROTEIN / DEP-domain / mTOR-binding / mTOR / mTORC1 / mTORC2 / DEPTOR
Function / homology
Function and homology information


negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / phosphatidic acid binding / negative regulation of TOR signaling / protein serine/threonine kinase inhibitor activity / negative regulation of cell size / protein kinase inhibitor activity / positive regulation of autophagy / negative regulation of TORC1 signaling / negative regulation of protein kinase activity ...negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / phosphatidic acid binding / negative regulation of TOR signaling / protein serine/threonine kinase inhibitor activity / negative regulation of cell size / protein kinase inhibitor activity / positive regulation of autophagy / negative regulation of TORC1 signaling / negative regulation of protein kinase activity / intracellular signal transduction / lysosomal membrane
Similarity search - Function
DEP domain-containing mTOR-interacting protein, DEP domain 1 / DEP domain-containing mTOR-interacting protein, DEP domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...DEP domain-containing mTOR-interacting protein, DEP domain 1 / DEP domain-containing mTOR-interacting protein, DEP domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DEP domain-containing mTOR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWaelchli, M. / Jakob, R. / Maier, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation179323 Switzerland
CitationJournal: Elife / Year: 2021
Title: Regulation of human mTOR complexes by DEPTOR.
Authors: Matthias Wälchli / Karolin Berneiser / Francesca Mangia / Stefan Imseng / Louise-Marie Craigie / Edward Stuttfeld / Michael N Hall / Timm Maier /
Abstract: The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein ...The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein that binds and regulates both complexes of mammalian target of rapamycin (mTOR), a central regulator of cell growth. Biochemical analysis and cryo-EM reconstructions of DEPTOR bound to human mTOR complex 1 (mTORC1) and mTORC2 reveal that both structured regions of DEPTOR, the PDZ domain and the DEP domain tandem (DEPt), are involved in mTOR interaction. The PDZ domain binds tightly with mildly activating effect, but then acts as an anchor for DEPt association that allosterically suppresses mTOR activation. The binding interfaces of the PDZ domain and DEPt also support further regulation by other signaling pathways. A separate, substrate-like mode of interaction for DEPTOR phosphorylation by mTOR complexes rationalizes inhibition of non-stimulated mTOR activity at higher DEPTOR concentrations. The multifaceted interplay between DEPTOR and mTOR provides a basis for understanding the divergent roles of DEPTOR in physiology and opens new routes for targeting the mTOR-DEPTOR interaction in disease.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DEP domain-containing mTOR-interacting protein
A: DEP domain-containing mTOR-interacting protein


Theoretical massNumber of molelcules
Total (without water)54,2582
Polymers54,2582
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS data shows t
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-27 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.862, 99.014, 68.245
Angle α, β, γ (deg.)90.000, 109.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 20 - 230 / Label seq-ID: 20 - 230

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBA

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Components

#1: Protein DEP domain-containing mTOR-interacting protein / DEP domain-containing protein 6


Mass: 27128.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEPTOR, DEPDC6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TB45
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 58.75 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350,natrium hydrochlorid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→99.01 Å / Num. obs: 46594 / % possible obs: 97.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.2
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 1.132 / Num. unique obs: 2829

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7Z

4f7z


Resolution: 1.93→53.903 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 1991 4.3 %
Rwork0.2106 44331 -
obs0.2113 46322 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.68 Å2 / Biso mean: 70.3279 Å2 / Biso min: 33.61 Å2
Refinement stepCycle: final / Resolution: 1.93→53.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 0 204 3776
Biso mean---56.97 -
Num. residues----422
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2190X-RAY DIFFRACTION10.78TORSIONAL
12B2190X-RAY DIFFRACTION10.78TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.97830.36991230.4144279685
1.9783-2.03180.33271400.3352305393
2.0318-2.09150.28831360.294317598
2.0915-2.15910.28771400.2683317398
2.1591-2.23620.2921480.2567319498
2.2362-2.32580.26831460.2393322298
2.3258-2.43160.2511490.2393320798
2.4316-2.55980.27051420.2442313396
2.5598-2.72020.27051340.2349321798
2.7202-2.93020.24791460.2472322599
2.9302-3.2250.28121540.2426322299
3.225-3.69160.24641450.2126318797
3.6916-4.65070.17981460.1731326899
4.6507-53.9030.1751420.1762325998
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)
11.4288-0.009-0.04030.8434-0.33751.3027-0.2677-0.37570.3816-0.0040.2459-0.0642-0.7707-0.0733-0.01140.54240.0809-0.04870.3524-0.14460.52140.9588-2.731222.6349
20.06920.1893-0.15480.5229-0.42450.3416-0.3684-0.8361-0.18150.09280.41450.364-0.4211-0.72560.00570.5510.17810.01490.7641-0.09940.563132.5386-7.320626.8698
30.854-0.29060.23220.4704-0.12240.0568-0.1317-0.25680.22730.25380.1477-0.053-0.09960.1378-0.00010.4640.0480.00680.4935-0.03970.471950.9675-21.103123.6645
41.9695-0.84010.79390.7645-1.16713.4493-0.27940.31190.27150.0401-0.2035-0.1975-0.71440.3788-0.00690.5277-0.1116-0.05490.43310.10040.55534.1819-2.4314-6.7174
50.16270.2299-0.20060.2549-0.27730.2419-0.23770.2292-0.1057-0.02940.1443-0.2870.2287-0.23460.00010.3849-0.0010.02340.3796-0.01780.430165.6456-26.695310.4262
60.47110.16180.33081.31830.22490.899-0.05650.0357-0.16160.25630.03720.09880.8084-0.3511-0.00050.5378-0.01660.03350.54870.01840.481154.6975-34.8525.9078
70.8772-1.08810.33111.2355-0.20640.4931-0.1854-0.44590.21830.27020.1286-0.0944-0.0312-0.0899-00.46530.023-0.00370.549-0.10090.460154.0113-17.684324.7594
81.8006-0.6109-0.11981.0978-0.11440.66860.07670.4879-0.1334-0.3148-0.13480.03280.3565-0.44940.00010.5793-0.01530.03140.5467-0.03860.414368.0927-29.3766-9.2681
91.1091-1.0064-0.51661.5066-0.1350.92640.35550.55950.0909-0.5599-0.24490.0971-0.3527-0.56350.00350.5370.1115-0.04350.72070.00570.415561.9066-22.4657-12.8708
100.3233-0.2001-0.23180.24190.30810.3880.03350.1869-0.074-0.1833-0.1095-0.20430.55530.2253-0.00020.49730.05340.06240.43270.01380.479571.8282-28.83013.8912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 20 through 81 )B20 - 81
2X-RAY DIFFRACTION2chain 'B' and (resid 82 through 94 )B82 - 94
3X-RAY DIFFRACTION3chain 'B' and (resid 95 through 127 )B95 - 127
4X-RAY DIFFRACTION4chain 'B' and (resid 128 through 230 )B128 - 230
5X-RAY DIFFRACTION5chain 'A' and (resid 20 through 46 )A20 - 46
6X-RAY DIFFRACTION6chain 'A' and (resid 47 through 81 )A47 - 81
7X-RAY DIFFRACTION7chain 'A' and (resid 82 through 127 )A82 - 127
8X-RAY DIFFRACTION8chain 'A' and (resid 128 through 166 )A128 - 166
9X-RAY DIFFRACTION9chain 'A' and (resid 167 through 214 )A167 - 214
10X-RAY DIFFRACTION10chain 'A' and (resid 215 through 230 )A215 - 230

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