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- PDB-9f0i: Human Cyclophilin D in complex with fragment -

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Basic information

Entry
Database: PDB / ID: 9f0i
TitleHuman Cyclophilin D in complex with fragment
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Cyclophilin D PPIase
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: 1.4 Å
AuthorsSilva, D.O. / Graedler, U. / Bandeiras, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Cyclophilin D in complex with fragment
Authors: Silva, D.O. / Graedler, U.
History
DepositionApr 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,0062
Polymers17,7821
Non-polymers2231
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7350 Å2
Unit cell
Length a, b, c (Å)58.294, 58.294, 113.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 17782.271 Da / Num. of mol.: 1 / Mutation: K125Q, K133I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Plasmid: pet28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-A1H8Q / ~{N}-(2-ethyl-1,2,3,4-tetrazol-5-yl)thiophene-2-carboxamide


Mass: 223.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 18 - 23 % PEG3350, 0.1 M TRIS-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.4→33.33 Å / Num. obs: 39031 / % possible obs: 99.01 % / Redundancy: 7.7 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.55
Reflection shellResolution: 1.4→1.451 Å / Num. unique obs: 3508 / CC1/2: 0.497

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.33 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.8355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 1971 5.08 %
Rwork0.1651 36861 -
obs0.1667 38832 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.7 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 15 259 1514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721293
X-RAY DIFFRACTIONf_angle_d0.89911744
X-RAY DIFFRACTIONf_chiral_restr0.083187
X-RAY DIFFRACTIONf_plane_restr0.0071229
X-RAY DIFFRACTIONf_dihedral_angle_d12.4512466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.47821480.42562255X-RAY DIFFRACTION87.86
1.44-1.470.29031200.28752621X-RAY DIFFRACTION99.53
1.47-1.520.26751300.18712622X-RAY DIFFRACTION99.96
1.52-1.570.25721350.15492613X-RAY DIFFRACTION100
1.57-1.620.21421310.15782623X-RAY DIFFRACTION99.96
1.62-1.690.2111520.15532607X-RAY DIFFRACTION99.93
1.69-1.760.19971420.15182643X-RAY DIFFRACTION100
1.77-1.860.20361400.14962630X-RAY DIFFRACTION99.93
1.86-1.970.18031580.15122615X-RAY DIFFRACTION99.93
1.97-2.130.19221450.16052661X-RAY DIFFRACTION99.89
2.13-2.340.16991270.14082673X-RAY DIFFRACTION99.86
2.34-2.680.16711460.15592677X-RAY DIFFRACTION99.65
2.68-3.370.18921310.16332742X-RAY DIFFRACTION99.97
3.38-33.330.19721660.1722879X-RAY DIFFRACTION99.57

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