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- PDB-9pj1: Crystal structure of a synthetic Fab (4R) in complex with the ter... -

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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


positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / 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 / macrolide binding / regulation of membrane permeability ...positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / 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 / macrolide binding / regulation of membrane permeability / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / voluntary musculoskeletal movement / activin receptor binding / negative regulation of lysosome organization / TORC1 complex / calcineurin-NFAT signaling cascade / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / cytoplasmic side of membrane / regulation of osteoclast differentiation / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / energy reserve metabolic process / MTOR signalling / regulation of lysosome organization / 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 / negative regulation of activin receptor signaling pathway / Amino acids regulate mTORC1 / signaling receptor inhibitor activity / heart trabecula formation / cellular response to methionine / negative regulation of cell size / TORC2 signaling / I-SMAD binding / cellular response to osmotic stress / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / cell projection organization / anoikis / inositol hexakisphosphate binding / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of ubiquitin-dependent protein catabolic process / regulation of myelination / negative regulation of protein localization to nucleus / positive regulation of transcription by RNA polymerase III / 'de novo' protein folding / positive regulation of ruffle assembly / regulation of cell size / ventricular cardiac muscle tissue morphogenesis / FK506 binding / positive regulation of myotube differentiation / negative regulation of macroautophagy / Macroautophagy / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / oligodendrocyte differentiation / TGF-beta receptor signaling activates SMADs / TORC1 signaling / positive regulation of oligodendrocyte differentiation / behavioral response to pain / response to amino acid / TOR signaling / mTORC1-mediated signalling / Calcineurin activates NFAT / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / positive regulation of translational initiation / regulation of macroautophagy / regulation of immune response / positive regulation of epithelial to mesenchymal transition / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lipid biosynthetic process / vascular endothelial cell response to laminar fluid shear stress / heart morphogenesis / regulation of cellular response to heat / positive regulation of lamellipodium assembly / neuronal action potential / T cell costimulation / phagocytic vesicle / positive regulation of stress fiber assembly / cardiac muscle contraction / supramolecular fiber organization / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cytoskeleton organization / negative regulation of insulin receptor signaling pathway / sarcoplasmic reticulum membrane / endomembrane system / cellular response to nutrient levels
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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)

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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

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Details

Has ligand of interestY
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: 55.15 %
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

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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

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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

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