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- PDB-4j5a: Human Cyclophilin D Complexed with an Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4j5a
TitleHuman Cyclophilin D Complexed with an Inhibitor
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsIsomerase/Isomerase Inhibitor / Isomerase-Isomerase Inhibitor complex
Function / homology
Function and homology information


regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / 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 / negative regulation of ATP-dependent activity / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / 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 / negative regulation of ATP-dependent activity / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / necroptotic process / apoptotic mitochondrial changes / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / peptide binding / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-67Z / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 1.58 Å
AuthorsGelin, M. / Colliandre, L. / Bessin, Y. / Guichou, J.F.
CitationJournal: to be published
Title: Rationnal Design of small-molecule inhibitors of human Cyclophilins and HCV replication.
Authors: Colliandre, L. / Hamed-Belkacem, H. / Gelin, M. / Bessin, Y. / Douguet, D. / Bourguet, W. / Pawlotsky, J.M. / Guichou, J.F.
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1433
Polymers17,6521
Non-polymers4912
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.090, 57.090, 88.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11X-595-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin F / Rotamase F


Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: UNP residues 44-207 / Mutation: K175I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3, PPIF / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-67Z / 1-(4-aminobenzyl)-3-{2-[(2R)-2-(2,5-dimethoxyphenyl)pyrrolidin-1-yl]-2-oxoethyl}urea


Mass: 412.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N4O4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 30% PEG4000, pH 7.3, vapor diffusion, hanging drop, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.58→36.697 Å / Num. all: 20616 / Num. obs: 20616 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.58-1.676.50.5081.50.508199
1.67-1.776.60.342.30.34199.7
1.77-1.896.60.1983.90.198199.8
1.89-2.046.60.1156.60.115199.9
2.04-2.236.50.0759.50.0751100
2.23-2.56.70.059120.0591100
2.5-2.886.70.04913.20.0491100
2.88-3.536.10.03715.80.0371100
3.53-56.60.02821.10.0281100
5-36.69770.025200.025199.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: Isomorphous Replacement / Resolution: 1.58→36.697 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.17 / σ(F): 1.15 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 1025 5.01 %
Rwork0.1416 --
obs0.144 20616 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.0722 Å2
Refinement stepCycle: LAST / Resolution: 1.58→36.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 34 236 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051346
X-RAY DIFFRACTIONf_angle_d1.151821
X-RAY DIFFRACTIONf_dihedral_angle_d11.33504
X-RAY DIFFRACTIONf_chiral_restr0.07195
X-RAY DIFFRACTIONf_plane_restr0.005236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.62280.27831530.24032650X-RAY DIFFRACTION96
1.6228-1.67060.26391270.21272720X-RAY DIFFRACTION97
1.6706-1.72450.26741520.20122705X-RAY DIFFRACTION97
1.7245-1.78610.22331590.17982694X-RAY DIFFRACTION98
1.7861-1.85760.26151450.15672720X-RAY DIFFRACTION98
1.8576-1.94220.1891340.1432743X-RAY DIFFRACTION98
1.9422-2.04460.23321650.12622735X-RAY DIFFRACTION99
2.0446-2.17260.17191490.11792750X-RAY DIFFRACTION99
2.1726-2.34040.18211300.11482774X-RAY DIFFRACTION99
2.3404-2.57580.16961230.13512804X-RAY DIFFRACTION99
2.5758-2.94840.18981600.13842715X-RAY DIFFRACTION99
2.9484-3.71410.15151370.12422731X-RAY DIFFRACTION98
3.7141-36.70710.14591400.13332789X-RAY DIFFRACTION99

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