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- PDB-6yf3: FKBP12 in complex with the BMP potentiator compound 10 at 1.00A r... -

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Basic information

Entry
Database: PDB / ID: 6yf3
TitleFKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / IMMUNOSUPPRESSION / IMMUNOSUPPRESSANT / BMP ENHANCER PROGRAM
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / Chem-OOZ / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsKallen, J.
CitationJournal: Cell Chem Biol / Year: 2021
Title: Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury.
Authors: Larraufie, M.H. / Gao, X. / Xia, X. / Devine, P.J. / Kallen, J. / Liu, D. / Michaud, G. / Harsch, A. / Savage, N. / Ding, J. / Tan, K. / Mihalic, M. / Roggo, S. / Canham, S.M. / Bushell, S.M. ...Authors: Larraufie, M.H. / Gao, X. / Xia, X. / Devine, P.J. / Kallen, J. / Liu, D. / Michaud, G. / Harsch, A. / Savage, N. / Ding, J. / Tan, K. / Mihalic, M. / Roggo, S. / Canham, S.M. / Bushell, S.M. / Krastel, P. / Gao, J. / Izaac, A. / Altinoglu, E. / Lustenberger, P. / Salcius, M. / Harbinski, F. / Williams, E.T. / Zeng, L. / Loureiro, J. / Cong, F. / Fryer, C.J. / Klickstein, L. / Tallarico, J.A. / Jain, R.K. / Rothman, D.M. / Wang, S.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9756
Polymers11,9911
Non-polymers9845
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-38 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.279, 57.279, 54.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-205-

NA

31A-399-

HOH

41A-408-

HOH

51A-423-

HOH

61A-436-

HOH

71A-438-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 11990.676 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 BL21 (bacteria) / References: UniProt: P62942, peptidylprolyl isomerase

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-OOZ / (1~{R},9~{S},12~{S},13~{R},14~{S},17~{R},18~{E},21~{S},23~{S},24~{R},25~{S},27~{R})-17-ethyl-25-methoxy-12-[(~{E})-1-[(1~{R},3~{R},4~{R})-3-methoxy-4-oxidanyl-cyclohexyl]prop-1-en-2-yl]-13,19,21,27-tetramethyl-1,14,23-tris(oxidanyl)-11,28-dioxa-4-azatricyclo[22.3.1.0^{4,9}]octacos-18-ene-2,3,10,16-tetrone


Mass: 777.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H67NO12 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 33.77 % / Mosaicity: 0.1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.2 M AmSO4, 0.2 M CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2015
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1→54.3 Å / Num. obs: 45824 / % possible obs: 94 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Net I/σ(I): 27.2 / Num. measured all: 496239
Reflection shellResolution: 1→1.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.1 / Num. measured all: 19309 / Num. unique obs: 5242 / CC1/2: 0.808 / Rpim(I) all: 0.229 / Rrim(I) all: 0.471 / Net I/σ(I) obs: 3.1 / % possible all: 68.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.3.3data scaling
PHASERphasing
REFMAC5.5.0063refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DH0

4dh0


Resolution: 1→40.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.601 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1582 2271 5 %RANDOM
Rwork0.1574 ---
obs0.1574 43503 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 39.28 Å2 / Biso mean: 12.409 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 59 142 1040
Biso mean--10.71 22.57 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.3622.0371340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1185126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93523.5939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.25615169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.811156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021731
X-RAY DIFFRACTIONr_rigid_bond_restr1.0533978
X-RAY DIFFRACTIONr_sphericity_free3.6123146
X-RAY DIFFRACTIONr_sphericity_bonded3.463944
LS refinement shellResolution: 1.004→1.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 116 -
Rwork0.274 1915 -
all-2031 -
obs--57.52 %

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