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- PDB-4drh: Co-crystal structure of the PPIase domain of FKBP51, Rapamycin an... -

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Basic information

Entry
Database: PDB / ID: 4drh
TitleCo-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of mTOR at low pH
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP5
  • Serine/threonine-protein kinase mTOR
KeywordsIsomerase/Transferase / Fk-506 binding domain / Hsp90 cochaperone / immunophilin / peptidyl-prolyl isomerase / mammalian target of Rapamycin / kinase / signalling / immunosuppression / cancer / Isomerase-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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / 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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / heart valve morphogenesis / negative regulation of lysosome organization / TFIIIC-class transcription factor complex binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / Amino acids regulate mTORC1 / cellular response to L-leucine / MTOR signalling / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / energy reserve metabolic process / ruffle organization / serine/threonine protein kinase complex / negative regulation of cell size / cellular response to methionine / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / response to alcohol / anoikis / negative regulation of protein localization to nucleus / Modulation of host responses by IFN-stimulated genes / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / positive regulation of actin filament polymerization / negative regulation of macroautophagy / regulation of cell size / Macroautophagy / FK506 binding / positive regulation of myotube differentiation / Constitutive Signaling by AKT1 E17K in Cancer / oligodendrocyte differentiation / germ cell development / behavioral response to pain / TOR signaling / mTORC1-mediated signalling / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / response to amino acid / HSF1-dependent transactivation / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to nutrient levels / vascular endothelial cell response to laminar fluid shear stress / neuronal action potential / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / regulation of cellular response to heat / positive regulation of lamellipodium assembly / MECP2 regulates neuronal receptors and channels / cardiac muscle contraction / phagocytic vesicle / positive regulation of stress fiber assembly / : / heat shock protein binding / T cell costimulation / cytoskeleton organization / endomembrane system / negative regulation of autophagy / cellular response to amino acid starvation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidyl-prolyl cis-trans isomerase activity / cellular response to starvation / positive regulation of glycolytic process / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / post-embryonic development / positive regulation of translation / VEGFR2 mediated vascular permeability / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / TP53 Regulates Metabolic Genes / peptidylprolyl isomerase / regulation of actin cytoskeleton organization / phosphoprotein binding / cellular response to amino acid stimulus
Similarity search - Function
FKBP12-rapamycin binding domain / 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 / Serine/threonine-protein kinase ATR-like, HEAT repeats / Rapamycin binding domain ...FKBP12-rapamycin binding domain / 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 / Serine/threonine-protein kinase ATR-like, HEAT repeats / Rapamycin binding domain / : / : / FATC domain / PIK-related kinase, FAT / FAT domain / Chitinase A; domain 3 - #40 / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Four Helix Bundle (Hemerythrin (Met), subunit A) / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Roll / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsMaerz, A.M. / Bracher, A. / Hausch, F.
CitationJournal: Mol.Cell.Biol. / Year: 2013
Title: Large FK506-Binding Proteins Shape the Pharmacology of Rapamycin.
Authors: Marz, A.M. / Fabian, A.K. / Kozany, C. / Bracher, A. / Hausch, F.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
B: Serine/threonine-protein kinase mTOR
D: Peptidyl-prolyl cis-trans isomerase FKBP5
E: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,72827
Polymers54,8824
Non-polymers3,84623
Water1,60389
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
B: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,41214
Polymers27,4412
Non-polymers1,97112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-123 kcal/mol
Surface area12300 Å2
MethodPISA
2
D: Peptidyl-prolyl cis-trans isomerase FKBP5
E: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,31613
Polymers27,4412
Non-polymers1,87511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-146 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.678, 103.678, 106.543
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-205-

SO4

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor- ...PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 15693.832 Da / Num. of mol.: 2 / Fragment: FKBP51 Fk1 domain, UNP RESIDUES 1-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIG6, FKBP5, FKBP51 / Plasmid: pProEx-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13451, 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


Mass: 11747.374 Da / Num. of mol.: 2 / Fragment: FRB domain, UNP RESIDUES 2025-2114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 / Plasmid: pProEx-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 914.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: immunosuppressant, antibiotic*YM
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.5
Details: 0.1M citric acid 2M (NH4)2SO4, pH 3.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.3→89.803 Å / Num. all: 29100 / Num. obs: 29100 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 46.27 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 18.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.427.50.5191.43151341760.51998.8
2.42-2.577.50.3352.22996839790.33599.2
2.57-2.757.50.2243.42819837720.22499.4
2.75-2.977.50.14652625535200.14699.7
2.97-3.257.40.08982395132350.08999.9
3.25-3.647.40.05711.92159329280.05799.9
3.64-4.27.30.05710.61896526040.05799.8
4.2-5.147.10.0688.21575122120.06899.6
5.14-7.276.90.05610.61168017050.05698.8
7.27-89.8037.20.03716.670179690.03797.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å89.79 Å
Translation3 Å89.79 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAP

1fap


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2467 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8532 / SU B: 12.061 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2816 / SU Rfree: 0.2124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1474 5.1 %RANDOM
Rwork0.1871 ---
obs0.1891 27545 99.36 %-
all-29019 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.55 Å2 / Biso mean: 45.9823 Å2 / Biso min: 22.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 235 89 3821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223819
X-RAY DIFFRACTIONr_angle_refined_deg1.452.025165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16924.479163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45715630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022821
X-RAY DIFFRACTIONr_nbd_refined0.1990.21590
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.215
X-RAY DIFFRACTIONr_mcbond_it0.5931.52291
X-RAY DIFFRACTIONr_mcangle_it0.8823535
X-RAY DIFFRACTIONr_scbond_it1.56731737
X-RAY DIFFRACTIONr_scangle_it2.2914.51630
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 100 -
Rwork0.232 1999 -
all-2099 -
obs--98.87 %
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)
14.23121.7298-0.09132.8622-0.21154.46520.0219-0.32620.23920.09090.05690.2318-0.401-0.4133-0.0787-0.23080.0649-0.0509-0.0358-0.0712-0.1436-26.06519.436-6.227
24.7102-0.60510.24436.05371.10886.42560.0922-0.1826-0.13350.3729-0.1624-0.2951-0.2068-0.14680.0701-0.3174-0.0433-0.0111-0.09940.0015-0.2394-12.7619.261.402
34.6791-0.0186-0.83454.04481.21585.9041-0.0298-0.03320.02520.0036-0.0457-0.0908-0.2540.03540.0755-0.2794-0.0235-0.04-0.1553-0.0101-0.2656-15.16819.82-4.905
45.61372.14021.91644.00551.40347.3642-0.0229-0.03520.1974-0.14320.02920.0312-0.59120.1967-0.0063-0.2615-0.10330.0247-0.07790.0017-0.22739.35321.822.322
58.76778.99244.880417.62762.9233.23250.5047-0.5133-0.41161.0733-0.5238-1.1718-0.51730.78680.01910.0653-0.2397-0.00360.3512-0.0031-0.160913.26924.67117.803
65.1383-1.8912-0.144213.41942.68464.01260.0021-0.7516-0.0305-0.09240.03480.03470.0069-0.0158-0.0369-0.3269-0.11310.0201-0.02520.0152-0.2892.7514.0847.836
79.97952.74772.6254.50140.39193.4526-0.08820.27990.5922-0.5123-0.04680.5607-0.4763-0.24870.1350.015-0.11530.0123-0.1202-0.0325-0.095331.3255.4074.411
87.44171.35122.26787.59120.8414.5794-0.22040.6936-0.1379-0.66390.17730.0547-0.12250.11570.0431-0.0057-0.22590.0297-0.024-0.0073-0.163728.13145.961-2.256
97.03731.0171.68796.7167-1.57486.52240.07560.0684-0.5692-0.26210.01520.19180.3922-0.0013-0.0907-0.0983-0.16190.0624-0.1257-0.0457-0.126529.34443.6494.163
105.56840.55190.04775.27391.60386.765-0.10190.3667-0.206-0.42850.07240.0977-0.0839-0.30490.0295-0.107-0.22810.0889-0.0743-0.0202-0.15615.98724.013-4.892
1110.3361-4.84535.10827.647-3.557210.68770.11330.2484-0.3738-1.25170.1919-0.55190.4287-0.3216-0.30520.076-0.29310.2299-0.0129-0.0618-0.087825.43823.287-11.893
127.5658-6.0987-1.52313.467-2.26849.4689-0.50160.86870.1086-1.14010.42390.1426-0.8319-0.16890.07770.0821-0.29190.0045-0.0125-0.0142-0.205720.72232.722-10.409
137.0578-2.4792.28163.55463.38187.2575-0.18430.2411-0.1201-0.61130.2124-0.3118-0.49040.0702-0.0281-0.2497-0.104-0.0573-0.1390.013-0.2056-4.93420.018-1.833
141.22263.41820.879310.8081.70211.08940.4182-0.3875-0.6364-0.1636-0.1416-0.2479-0.56670.1065-0.2766-0.119-0.18250.00670.0781-0.1067-0.10423.83336.969-0.293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 48
2X-RAY DIFFRACTION2A49 - 86
3X-RAY DIFFRACTION3A87 - 140
4X-RAY DIFFRACTION4B2018 - 2056
5X-RAY DIFFRACTION5B2057 - 2076
6X-RAY DIFFRACTION6B2077 - 2112
7X-RAY DIFFRACTION7D10 - 51
8X-RAY DIFFRACTION8D52 - 101
9X-RAY DIFFRACTION9D102 - 140
10X-RAY DIFFRACTION10E2019 - 2066
11X-RAY DIFFRACTION11E2067 - 2097
12X-RAY DIFFRACTION12E2098 - 2112
13X-RAY DIFFRACTION13A201
14X-RAY DIFFRACTION14D201

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