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- PDB-9dl0: Crystal structure of a synthetic Fab (R3H8) in complex with the F... -

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Basic information

Entry
Database: PDB / ID: 9dl0
TitleCrystal structure of a synthetic Fab (R3H8) in complex with the FRB domain of mTOR
Components
  • Fab heavy chain
  • Fab light chain
  • Serine/threonine-protein kinase mTOR
KeywordsIMMUNE SYSTEM/Transferase / kinase / inhibitor / antibody / signaling protein / IMMUNE SYSTEM / IMMUNE SYSTEM-Transferase complex
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / regulation of lysosome organization / MTOR signalling / cellular response to nutrient / cellular response to L-leucine / Amino acids regulate mTORC1 / energy reserve metabolic process / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / inositol hexakisphosphate binding / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / TOR signaling / behavioral response to pain / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of macroautophagy / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / vascular endothelial cell response to laminar fluid shear stress / positive regulation of lipid biosynthetic process / heart morphogenesis / cellular response to nutrient levels / neuronal action potential / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / phagocytic vesicle / T cell costimulation / positive regulation of stress fiber assembly / cytoskeleton organization / endomembrane system / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy / cellular response to amino acid starvation / positive regulation of translation / regulation of signal transduction by p53 class mediator / positive regulation of glycolytic process / cellular response to starvation / Regulation of PTEN gene transcription / VEGFR2 mediated vascular permeability / post-embryonic development / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / non-specific protein-tyrosine kinase / macroautophagy / response to nutrient levels / phosphoprotein binding / regulation of cell growth / regulation of circadian rhythm / PML body / protein destabilization / response to virus / multicellular organism growth / cellular response to insulin stimulus / Regulation of TP53 Degradation
Similarity search - Function
Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / : ...Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsO'Leary, K.M. / Slezak, T. / Kossiakoff, A.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution.
Authors: O'Leary, K.M. / Slezak, T. / Kossiakoff, A.A.
History
DepositionSep 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab heavy chain
G: Serine/threonine-protein kinase mTOR
H: Fab heavy chain
I: Serine/threonine-protein kinase mTOR
Y: Fab light chain
Z: Fab light chain


Theoretical massNumber of molelcules
Total (without water)116,4506
Polymers116,4506
Non-polymers00
Water6,720373
1
A: Fab heavy chain
G: Serine/threonine-protein kinase mTOR
Y: Fab light chain


Theoretical massNumber of molelcules
Total (without water)58,2253
Polymers58,2253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-35 kcal/mol
Surface area23390 Å2
MethodPISA
2
H: Fab heavy chain
I: Serine/threonine-protein kinase mTOR
Z: Fab light chain


Theoretical massNumber of molelcules
Total (without water)58,2253
Polymers58,2253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-37 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.613, 110.042, 131.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11Z-342-

HOH

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Components

#1: Antibody Fab heavy chain


Mass: 23536.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


Mass: 11606.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#3: Antibody Fab light chain


Mass: 23082.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5 4% PEG 400 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→110.2 Å / Num. obs: 82556 / % possible obs: 95.8 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 8485 / CC1/2: 0.295

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Processing

Software
NameVersionClassification
PHENIX(1.21.1)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.31 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 4198 5.16 %
Rwork0.205 --
obs0.2065 81284 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8113 0 0 373 8486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.014
X-RAY DIFFRACTIONf_dihedral_angle_d18.1432961
X-RAY DIFFRACTIONf_chiral_restr0.0611240
X-RAY DIFFRACTIONf_plane_restr0.0071434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.36811630.3282658X-RAY DIFFRACTION100
2.02-2.050.36721490.33162690X-RAY DIFFRACTION100
2.05-2.070.33191810.31162620X-RAY DIFFRACTION100
2.07-2.10.39411580.31032697X-RAY DIFFRACTION100
2.1-2.130.35651450.30852683X-RAY DIFFRACTION100
2.13-2.150.32391430.28922710X-RAY DIFFRACTION100
2.15-2.190.28291360.27332704X-RAY DIFFRACTION100
2.19-2.220.32821200.28722681X-RAY DIFFRACTION99
2.22-2.230.4433520.4238852X-RAY DIFFRACTION73
2.27-2.290.671330.4782671X-RAY DIFFRACTION50
2.29-2.330.30751340.28122681X-RAY DIFFRACTION100
2.33-2.370.28291670.2762698X-RAY DIFFRACTION100
2.37-2.420.31071450.23842693X-RAY DIFFRACTION100
2.42-2.470.23331450.24042725X-RAY DIFFRACTION100
2.47-2.520.32451280.23462703X-RAY DIFFRACTION100
2.52-2.580.29521430.22492714X-RAY DIFFRACTION100
2.58-2.640.27471540.21612692X-RAY DIFFRACTION100
2.64-2.710.26491470.22122713X-RAY DIFFRACTION100
2.71-2.790.27811310.21692734X-RAY DIFFRACTION100
2.79-2.880.28091610.22432698X-RAY DIFFRACTION100
2.88-2.990.26161420.23422731X-RAY DIFFRACTION100
2.99-3.110.2431560.21122713X-RAY DIFFRACTION100
3.11-3.250.22161400.20782756X-RAY DIFFRACTION100
3.25-3.420.22441590.20192728X-RAY DIFFRACTION100
3.42-3.630.20961520.18482738X-RAY DIFFRACTION100
3.63-3.910.23361060.17632116X-RAY DIFFRACTION77
3.91-4.310.1741510.16212748X-RAY DIFFRACTION99
4.31-4.930.17071650.14212775X-RAY DIFFRACTION100
4.93-6.210.1821610.17452798X-RAY DIFFRACTION100
6.21-56.310.20181310.18092966X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.1836 Å / Origin y: -29.4808 Å / Origin z: -23.5179 Å
111213212223313233
T0.2196 Å20.0007 Å2-0.0038 Å2-0.2343 Å20.0107 Å2--0.251 Å2
L0.0863 °20.0272 °20.0233 °2-0.0551 °2-0.0028 °2--0.3561 °2
S0.002 Å °0.0211 Å °0.032 Å °-0.0146 Å °-0.0014 Å °0.0374 Å °-0.0204 Å °-0.0128 Å °-0 Å °
Refinement TLS groupSelection details: all

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