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- PDB-8uc5: Apo X-ray crystal structure of Cyclophilin D with a surface entro... -

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Basic information

Entry
Database: PDB / ID: 8uc5
TitleApo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Peptidyl prolyl isomerase / Cyclophilin D / mitochondria
Function / homology
Function and homology information


: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / necroptotic process / apoptotic mitochondrial changes / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsKreitler, D.F. / Rangwala, A.M. / Seeliger, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119437 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F30CA260771 United States
CitationJournal: To Be Published
Title: Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
Authors: Kreitler, D.F. / Seeliger, M.A. / Rangwala, A.M.
History
DepositionSep 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
B: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,61419
Polymers53,6023
Non-polymers1,01216
Water6,287349
1
X: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,43010
Polymers17,8671
Non-polymers5639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1606
Polymers17,8671
Non-polymers2935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0243
Polymers17,8671
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.667, 56.643, 101.172
Angle α, β, γ (deg.)90.000, 123.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CyP-D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17867.334 Da / Num. of mol.: 3 / Mutation: K175I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.73 % / Description: 3D
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Well solution: 2.1 M DL-Malic acid pH 7.0. Protein solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol. Drop: 1 uL protein, 1 uL well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2022 / Details: KB
RadiationMonochromator: DCM Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.43→29.33 Å / Num. obs: 105128 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.24 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.093 / Net I/σ(I): 8.8
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7331 / CC1/2: 0.657 / Rrim(I) all: 0.807 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
DIMPLEphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→29.33 Å / SU ML: 0.1273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 1996 1.9 %
Rwork0.1442 103124 -
obs0.1448 105120 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.71 Å2
Refinement stepCycle: LAST / Resolution: 1.43→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 49 349 4139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013916
X-RAY DIFFRACTIONf_angle_d1.12245285
X-RAY DIFFRACTIONf_chiral_restr0.095576
X-RAY DIFFRACTIONf_plane_restr0.0058687
X-RAY DIFFRACTIONf_dihedral_angle_d11.51281414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.460.2571310.21117001X-RAY DIFFRACTION92.89
1.46-1.50.24191440.19087292X-RAY DIFFRACTION96.75
1.5-1.550.23251470.17417260X-RAY DIFFRACTION96.84
1.55-1.60.2461340.16367291X-RAY DIFFRACTION97.07
1.6-1.660.19121390.15137343X-RAY DIFFRACTION97.32
1.66-1.720.1891350.13827357X-RAY DIFFRACTION97.49
1.72-1.80.19471480.12987342X-RAY DIFFRACTION97.69
1.8-1.890.15441440.12367418X-RAY DIFFRACTION98.03
1.89-2.010.15651390.12167368X-RAY DIFFRACTION97.98
2.01-2.170.15651530.1217402X-RAY DIFFRACTION98.05
2.17-2.390.18191360.13037427X-RAY DIFFRACTION98.25
2.39-2.730.181440.15517412X-RAY DIFFRACTION97.62
2.73-3.440.19661470.14887508X-RAY DIFFRACTION98.56
3.44-29.330.14151550.14727703X-RAY DIFFRACTION99.3

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