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- PDB-1fkr: SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK... -

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Basic information

Entry
Database: PDB / ID: 1fkr
TitleSOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN
ComponentsFK506 AND RAPAMYCIN-BINDING PROTEIN
KeywordsCIS-TRANS ISOMERASE
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / heart trabecula formation / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / signaling receptor inhibitor activity ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / heart trabecula formation / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / signaling receptor inhibitor activity / I-SMAD binding / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / FK506 binding / ventricular cardiac muscle tissue morphogenesis / TGF-beta receptor signaling activates SMADs / heart morphogenesis / mTORC1-mediated signalling / Calcineurin activates NFAT / regulation of immune response / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / peptidylprolyl isomerase / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / protein maturation / negative regulation of transforming growth factor beta receptor signaling pathway / protein refolding / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / Potential therapeutics for SARS / amyloid fibril formation / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsMichnick, S.W. / Rosen, M.K. / Wandless, T.J. / Karplus, M. / Schreiber, S.L.
Citation
Journal: Science / Year: 1991
Title: Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin.
Authors: Michnick, S.W. / Rosen, M.K. / Wandless, T.J. / Karplus, M. / Schreiber, S.L.
#1: Journal: Biochemistry / Year: 1991
Title: Proton and Nitrogen Sequential Assignments and Secondary Structure Determination of the Human Fk506 and Rapamycin Binding Protein
Authors: Rosen, M.K. / Michnick, S.W. / Karplus, M. / Schreiber, S.L.
#2: Journal: Nature / Year: 1990
Title: Molecular Cloning and Overexpression of the Human Fk506-Binding Protein Fkbp
Authors: Standaert, R.F. / Galat, A. / Verdine, G.L. / Schreiber, S.L.
History
DepositionMar 5, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506 AND RAPAMYCIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,8371
Polymers11,8371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: THE LIGAND BINDING SITE IS LINED BY A NUMBER OF CONSERVED AROMATIC AND ALIPHATIC RESIDUES. THESE ARE TYR 26, PHE 36, PHE 46, VAL 55, ILE 56, TRP 59, TYR 82 AND PHE 99.
2: THE +3, +1, -3, +1 TOPOLOGY OF THE FKBP12 BETA-SHEET RESULTS IN A CROSSING OF TWO STRAND-CONNECTING LOOPS (PRO 9 TO CYS 20, AND MET 66 TO GLN 70). TO THE BEST OF OUR KNOWLEDGE, THIS WAS THE FIRST ...2: THE +3, +1, -3, +1 TOPOLOGY OF THE FKBP12 BETA-SHEET RESULTS IN A CROSSING OF TWO STRAND-CONNECTING LOOPS (PRO 9 TO CYS 20, AND MET 66 TO GLN 70). TO THE BEST OF OUR KNOWLEDGE, THIS WAS THE FIRST EXAMPLE OF SUCH A STRUCTURE. INTERESTINGLY, THE RECENTLY-REPORTED STRUCTURE OF ANOTHER IMMUNOPHILIN (IMMUNO-SUPPRESSANT-BINDING PROTEIN), CYCLOPHILIN, ALSO CONTAINS THIS TYPE OF TOPOLOGICAL CROSSING OF TWO STRAND-CONNECTING LOOPS. THE SIGNIFICANCE OF THIS SIMILARITY, IF ANY, REMAINS UNKNOWN.
3: THE LOOPS FROM SER 39 TO LYS 44, AND ALA 83 TO HIS 94 ARE UNDERDETERMINED IN COMPARISON TO THE REMAINDER OF THE STRUCTURE. IN THE CRYSTAL STRUCTURES OF THE FKBP12-FK506 AND FKBP12-RAPAMYCIN ...3: THE LOOPS FROM SER 39 TO LYS 44, AND ALA 83 TO HIS 94 ARE UNDERDETERMINED IN COMPARISON TO THE REMAINDER OF THE STRUCTURE. IN THE CRYSTAL STRUCTURES OF THE FKBP12-FK506 AND FKBP12-RAPAMYCIN COMPLEXES, THE LATTER LOOP IS WELL DEFINED, AND MAKES NUMEROUS CONTACTS TO THE BOUND LIGANDS. WE ARE CURRENTLY IN THE PROCESS OF PERFORMING HETERONUCLEAR NOE AND RELAXATION EXPERIMENTS TO ANALYZE THE CHANGES IN MOBILITY OF THIS REGION UPON LIGAND-BINDING.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein FK506 AND RAPAMYCIN-BINDING PROTEIN


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: S2 / References: UniProt: P62942

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

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