[English] 日本語
Yorodumi
- PDB-9dl0: Crystal structure of a synthetic Fab (R3H8) in complex with the F... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / voluntary musculoskeletal movement / calcineurin-NFAT signaling cascade / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / MTOR signalling / Amino acids regulate mTORC1 / cellular response to L-leucine / cellular response to nutrient / 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 / inositol hexakisphosphate binding / cellular response to osmotic stress / anoikis / negative regulation of protein localization to nucleus / cardiac muscle cell development / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / positive regulation of actin filament polymerization / Constitutive Signaling by AKT1 E17K in Cancer / 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 / heart morphogenesis / vascular endothelial cell response to laminar fluid shear stress / neuronal action potential / positive regulation of lipid biosynthetic process / cellular response to nutrient levels / 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 autophagy / negative regulation of insulin receptor signaling pathway / cellular response to amino acid starvation / cellular response to starvation / positive regulation of glycolytic process / positive regulation of translation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / VEGFR2 mediated vascular permeability / post-embryonic development / response to nutrient levels / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / phosphoprotein binding / cellular response to amino acid stimulus / macroautophagy / regulation of cell growth / non-specific protein-tyrosine kinase / regulation of circadian rhythm / protein destabilization / PML body / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more