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- PDB-6yf2: FKBP12 in complex with the BMP potentiator compound 6 at 1.03A re... -

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Basic information

Entry
Database: PDB / ID: 6yf2
TitleFKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / IMMUNOSUPPRESSION / IMMUNOSUPPRESSANT / BMP ENHANCER PROGRAM
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 / signaling receptor inhibitor activity / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation ...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 / signaling receptor inhibitor activity / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / ventricular cardiac muscle tissue morphogenesis / protein maturation by protein folding / 'de novo' protein folding / FK506 binding / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of immune response / regulation of ryanodine-sensitive calcium-release channel activity / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / calcium ion transmembrane transport / Z disc / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein folding / regulation of protein localization / protein refolding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / amyloid fibril formation / Potential therapeutics for SARS / 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-OP5 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.03 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)13,0176
Polymers11,9911
Non-polymers1,0265
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-37 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.482, 57.482, 54.469
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-409-

HOH

41A-436-

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, 149 molecules

#2: Chemical ChemComp-OP5 / (1~{R},9~{S},12~{S},13~{R},14~{S},17~{R},18~{E},21~{S},23~{S},24~{R},25~{S},27~{R})-23,25-dimethoxy-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-bis(oxidanyl)-17-(2-oxidanylidenepropyl)-11,28-dioxa-4-azatricyclo[22.3.1.0^{4,9}]octacos-18-ene-2,3,10,16-tetrone


Mass: 820.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO13 / 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


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.88 Å3/Da / Density % sol: 34.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.9 M AmSO4, 0.15 M CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.03→19.77 Å / Num. obs: 44575 / % possible obs: 97.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Net I/σ(I): 32.8
Reflection shellResolution: 1.03→1.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 2585 / Rrim(I) all: 0.166 / % possible all: 78.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4dh0


Resolution: 1.03→19.77 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.512 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1488 2229 5 %RANDOM
Rwork0.1409 ---
obs0.1413 42347 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 42.76 Å2 / Biso mean: 10.47 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.03→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 62 144 1045
Biso mean--8.43 20.49 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022996
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.0451366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9223.8142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38715175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.28157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021754
X-RAY DIFFRACTIONr_rigid_bond_restr0.8643996
X-RAY DIFFRACTIONr_sphericity_free3.513148
X-RAY DIFFRACTIONr_sphericity_bonded3.1783961
LS refinement shellResolution: 1.03→1.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.138 129 -
Rwork0.118 2456 -
all-2585 -
obs--78.36 %

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