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- PDB-7u8d: FKBP12 mutant V55G bound to Rapa*-3Z -

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Basic information

Entry
Database: PDB / ID: 7u8d
TitleFKBP12 mutant V55G bound to Rapa*-3Z
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE/ISOMERASE INHIBITOR / immunophilin / rotamase / protein binding / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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 ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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 / signaling receptor inhibitor activity / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / protein maturation / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
: / 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
Similarity search - Domain/homology
Chem-LWR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsWassarman, D.R. / Shokat, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Tissue-restricted inhibition of mTOR using chemical genetics.
Authors: Wassarman, D.R. / Bankapalli, K. / Pallanck, L.J. / Shokat, K.M.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9966
Polymers23,8972
Non-polymers2,0994
Water5,332296
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9983
Polymers11,9491
Non-polymers1,0492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9983
Polymers11,9491
Non-polymers1,0492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.683, 44.138, 44.403
Angle α, β, γ (deg.)112.140, 97.040, 104.570
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 11948.597 Da / Num. of mol.: 2 / Mutation: V55G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Chemical ChemComp-LWR / (3S,5Z,6R,7E,9R,10R,12R,14S,15E,17E,19E,21S,23S,26R,27R,30R,34aS)-5-(ethoxyimino)-9,27-dihydroxy-3-{(2R)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl}-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-5,6,9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-octadecahydro-3H-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontine-1,11,28,29(4H,31H)-tetrone


Mass: 957.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H84N2O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: sodium tartrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→36.6 Å / Num. obs: 46706 / % possible obs: 93.22 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.91 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03888 / Rpim(I) all: 0.02356 / Rrim(I) all: 0.04557 / Net I/σ(I): 18.42
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4217 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 4275 / CC1/2: 0.825 / CC star: 0.951 / Rpim(I) all: 0.2585 / Rrim(I) all: 0.496 / % possible all: 85.18

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FKB

1fkb


Resolution: 1.39→36.6 Å / SU ML: 0.1278 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.3093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1723 1705 3.65 %
Rwork0.1468 44999 -
obs0.1477 46704 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.76 Å2
Refinement stepCycle: LAST / Resolution: 1.39→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 80 296 2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01541864
X-RAY DIFFRACTIONf_angle_d1.43332516
X-RAY DIFFRACTIONf_chiral_restr0.0879272
X-RAY DIFFRACTIONf_plane_restr0.0085322
X-RAY DIFFRACTIONf_dihedral_angle_d15.5768262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.430.23371260.17533366X-RAY DIFFRACTION83.5
1.43-1.480.20351480.16733762X-RAY DIFFRACTION93.45
1.48-1.530.22091380.15733769X-RAY DIFFRACTION93.74
1.53-1.590.17351510.14333756X-RAY DIFFRACTION94.1
1.59-1.660.18241390.14433834X-RAY DIFFRACTION94.51
1.66-1.750.19711510.13983754X-RAY DIFFRACTION94.35
1.75-1.860.16941370.13793778X-RAY DIFFRACTION93.26
1.86-20.17081400.13763781X-RAY DIFFRACTION93.87
2-2.210.161470.13583752X-RAY DIFFRACTION93.19
2.21-2.530.15871390.14363751X-RAY DIFFRACTION93.71
2.53-3.180.16361440.15093799X-RAY DIFFRACTION94.24
3.18-36.60.17141450.15133897X-RAY DIFFRACTION96.88

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