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- PDB-1fkl: ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPP... -

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Basic information

Entry
Database: PDB / ID: 1fkl
TitleATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
ComponentsFK506 BINDING PROTEINFKBP
KeywordsROTAMASE / FK506 BINDING PROTEIN / FKBP12 / FKBP / CIS-TRANS PROLYL-ISOMERASE
Function / homology
Function and homology information


mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / cytoplasmic side of membrane / activin binding / heart trabecula formation / negative regulation of release of sequestered calcium ion into cytosol / ryanodine receptor complex / regulation of amyloid precursor protein catabolic process ...mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / cytoplasmic side of membrane / activin binding / heart trabecula formation / negative regulation of release of sequestered calcium ion into cytosol / ryanodine receptor complex / regulation of amyloid precursor protein catabolic process / response to caffeine / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / SMAD binding / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / calcium channel inhibitor activity / protein peptidyl-prolyl isomerization / supramolecular fiber organization / T cell proliferation / heart morphogenesis / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / negative regulation of protein phosphorylation / sarcoplasmic reticulum / muscle contraction / peptidylprolyl isomerase / positive regulation of protein ubiquitination / peptidyl-prolyl cis-trans isomerase activity / Z disc / cytokine-mediated signaling pathway / regulation of protein localization / positive regulation of protein binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / amyloid fibril formation / protein homodimerization activity / extracellular exosome / membrane / cytosol / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWilson, K.P. / Sintchak, M.D. / Thomson, J.A. / Navia, M.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin.
Authors: Wilson, K.P. / Yamashita, M.M. / Sintchak, M.D. / Rotstein, S.H. / Murcko, M.A. / Boger, J. / Thomson, J.A. / Fitzgibbon, M.J. / Black, J.R. / Navia, M.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: X-Ray Structure of Calcineurin Inhibited by the Immunophilin-Immunosuppressant Fkbp12-Fk506 Complex
Authors: Griffith, J.P. / Kim, J.L. / Kim, E.E. / Sintchak, M.D. / Thomson, J.A. / Fitzgibbon, M.J. / Fleming, M.A. / Caron, P.R. / Hsiao, K. / Navia, M.A.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Improved Calcineurin Inhibition by Yeast Fkbp12-Drug Complexes
Authors: Rotonda, J. / Burbaum, J.J. / Chan, H.K. / Marcy, A.I. / Becker, J.W.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Fk-506-Binding Protein: Three-Dimensional Structure of the Complex with the Antagonist L-685,818
Authors: Becker, J.W. / Rotonda, J. / Mckeever, B.M. / Chan, H.K. / Marcy, A.I. / Wiederrecht, G. / Hermes, J.D. / Springer, J.P.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Atomic Structures of Human Immunophilin Fkbp12 Complexes with Fk506 and Rapamycin
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
#5: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
Authors: Van Duyne, G.D. / Standaert, R.F. / Schreiber, S.L. / Clardy, J.
#6: Journal: Science / Year: 1991
Title: Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
History
DepositionAug 18, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7092
Polymers11,7941
Non-polymers9141
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.900, 49.500, 55.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FK506 BINDING PROTEIN / FKBP / FKBP12 / FKBP


Mass: 11794.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MR 12,000 DALTONS / Source: (natural) Bos taurus (cattle) / Organ: THYMUS / References: UniProt: P18203, peptidylprolyl isomerase
#2: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Sirolimus


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: immunosuppressant, antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein 1drop
250 mMammonium sulfate1reservoir
3200 mMpotassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorDetector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MANUFACTURERSUPPLIED (MSC)data reduction
X-PLORphasing
RefinementResolution: 1.7→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.181 -
obs0.181 11083
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 65 63 958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.24

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