[English] 日本語
Yorodumi
- PDB-9pj1: Crystal structure of a synthetic Fab (4R) in complex with the ter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pj1
TitleCrystal structure of a synthetic Fab (4R) in complex with the ternary assembly of FKBP12, Rapamycin, and the FRB domain of mTOR
Components
  • Heavy chain
  • Light chain
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Serine/threonine-protein kinase mTOR
KeywordsIMMUNE SYSTEM/Transferase/Isomerase / Antibody / mTOR / rapamycin / sensor / IMMUNE SYSTEM / IMMUNE SYSTEM-Transferase-Isomerase complex
Function / homology
Function and homology information


cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / macrolide binding ...cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / macrolide binding / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of lysosome organization / activin receptor binding / TORC1 complex / negative regulation of lysosome organization / regulation of osteoclast differentiation / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / transforming growth factor beta receptor binding / heart trabecula formation / TGFBR1 LBD Mutants in Cancer / MTOR signalling / cytoplasmic side of membrane / cellular response to L-leucine / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / regulation of autophagosome assembly / type I transforming growth factor beta receptor binding / Amino acids regulate mTORC1 / negative regulation of activin receptor signaling pathway / signaling receptor inhibitor activity / Dengue virus modulates apoptosis / cellular response to methionine / TORC2 signaling / I-SMAD binding / cellular response to osmotic stress / regulation of amyloid precursor protein catabolic process / TORC1 signaling / anoikis / inositol hexakisphosphate binding / terminal cisterna / ryanodine receptor complex / negative regulation of protein localization to nucleus / positive regulation of ubiquitin-dependent protein catabolic process / regulation of cell size / negative regulation of macroautophagy / 'de novo' protein folding / FK506 binding / ventricular cardiac muscle tissue morphogenesis / Macroautophagy / Constitutive Signaling by AKT1 E17K in Cancer / behavioral response to pain / positive regulation of transcription by RNA polymerase III / positive regulation of protein kinase activity / TGF-beta receptor signaling activates SMADs / response to amino acid / neuronal action potential / TOR signaling / heart morphogenesis / mTORC1-mediated signalling / Calcineurin activates NFAT / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of immune response / positive regulation of translational initiation / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / T cell costimulation / vascular endothelial cell response to laminar fluid shear stress / regulation of cellular response to heat / cellular response to nutrient levels / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / cytoskeleton organization / negative regulation of insulin receptor signaling pathway / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phagocytic vesicle / supramolecular fiber organization / endomembrane system / sarcoplasmic reticulum membrane / positive regulation of glycolytic process / negative regulation of autophagy / cellular response to amino acid stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of signal transduction by p53 class mediator / cellular response to amino acid starvation / cellular response to starvation / Regulation of PTEN gene transcription / phosphatidylinositol 3-kinase/protein kinase B signal transduction / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / positive regulation of translation / TP53 Regulates Metabolic Genes / T cell activation / peptidylprolyl isomerase / sarcoplasmic reticulum
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. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsO'Leary, K.M. / Slezak, T. / Kossiakoff, A.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of FKBP12, Rapamycin, and the FRB domain of mTOR
Authors: O'Leary, K.M. / Slezak, T. / Kossiakoff, A.A.
History
DepositionJul 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Peptidyl-prolyl cis-trans isomerase FKBP1A
D: Serine/threonine-protein kinase mTOR
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9625
Polymers70,0484
Non-polymers9141
Water9,026501
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.720, 72.860, 85.900
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules CD

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11923.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#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 / Tyrosine-protein kinase mTOR


Mass: 11161.728 Da / Num. of mol.: 1
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, non-specific protein-tyrosine kinase

-
Antibody , 2 types, 2 molecules HL

#3: Antibody Heavy chain


Mass: 23965.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Light chain


Mass: 22996.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 502 molecules

#5: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
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: 55.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.15 M Ammonium sulfate, 0.1 M TRIS pH 8.0, 17.5% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→61.18 Å / Num. obs: 46596 / % possible obs: 98.14 % / Redundancy: 1.9 % / CC1/2: 0.993 / Net I/σ(I): 4.96
Reflection shellResolution: 2.05→2.09 Å / Mean I/σ(I) obs: 1.33 / Num. unique obs: 4625 / CC1/2: 0.363

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (REFMACAT 0.4.105)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→61.18 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.83 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / ESU R: 0.206 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2287 2286 4.9 %
Rwork0.1985 --
obs-46587 98.16 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-0.56 Å2
2--1.5 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.05→61.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 65 501 5466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0165086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164693
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.8016898
X-RAY DIFFRACTIONr_angle_other_deg0.3181.56110865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685.191656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.61959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6510833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021152
X-RAY DIFFRACTIONr_nbd_refined0.1760.2800
X-RAY DIFFRACTIONr_nbd_other0.1310.246
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22431
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2483
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_it2.5862.132539
X-RAY DIFFRACTIONr_mcbond_other2.5812.132538
X-RAY DIFFRACTIONr_mcangle_it4.1263.8163165
X-RAY DIFFRACTIONr_mcangle_other4.1263.8173166
X-RAY DIFFRACTIONr_scbond_it3.3522.4842547
X-RAY DIFFRACTIONr_scbond_other3.3512.4842548
X-RAY DIFFRACTIONr_scangle_it5.2274.3793733
X-RAY DIFFRACTIONr_scangle_other5.2274.383734
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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)
11.1737-0.0803-1.01970.1932-0.07861.71570.07140.01320.1338-0.036-0.0081-0.0794-0.08370.1509-0.06340.2005-0.0020.05140.05080.0060.046912.716-10.76.239
21.12040.129-1.08860.4221-0.15811.4814-0.00170.0115-0.0845-0.0291-0.0665-0.07770.09510.08360.06810.23480.03670.03010.05240.00620.022813.327-26.176-3.149
31.0790.0295-1.27851.3442-0.51966.0216-0.0102-0.05140.02310.1022-0.08020.0269-0.03980.0040.09050.1496-0.01710.00130.06530.0140.0114-13.339-22.63346.791
44.6365-0.9144-0.72331.6730.17732.1035-0.0808-0.21170.12970.08770.09440.2303-0.0016-0.3022-0.01360.162-0.00690.03040.11910.00650.0508-30.463-11.14332.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 227
2X-RAY DIFFRACTION2L2 - 214
3X-RAY DIFFRACTION3C1 - 108
4X-RAY DIFFRACTION4D1 - 92

+
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