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- PDB-4j58: Human Cyclophilin D Complexed with an Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4j58
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


: / : / 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-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-53Z / PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 1.28 Å
AuthorsColliandre, L. / Gelin, M. / Bessin, Y. / Guichou, J.F.
CitationJournal: Nat Commun / Year: 2016
Title: Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.
Authors: Ahmed-Belkacem, A. / Colliandre, L. / Ahnou, N. / Nevers, Q. / Gelin, M. / Bessin, Y. / Brillet, R. / Cala, O. / Douguet, D. / Bourguet, W. / Krimm, I. / 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 1.1Oct 19, 2016Group: Database references
Revision 1.2Feb 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
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0233
Polymers17,6521
Non-polymers3712
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.244, 57.244, 87.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-53Z / 1-(4-aminobenzyl)-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea


Mass: 276.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 39.5 %
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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2009
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.28→34.794 Å / Num. all: 36804 / Num. obs: 36804 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.28-1.352.10.3232.1883842080.32377.2
1.35-1.432.80.2133.31381349760.21396.2
1.43-1.533.90.1395.21921648810.13999.8
1.53-1.654.20.0957.71935545850.095100
1.65-1.814.10.0612.11730742330.06100
1.81-2.023.90.035201495738550.035100
2.02-2.343.80.02426.21307134290.024100
2.34-2.863.80.021271111529340.021100
2.86-4.053.60.01729.6827023250.017100
4.05-34.79430.01919416713780.01999.6

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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: 1.28→34.794 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.11 / σ(F): 0.93 / Phase error: 13.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1578 1825 5.03 %RANDOM
Rwork0.1193 ---
obs0.1212 36804 87.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.04 Å2 / Biso mean: 10.2844 Å2 / Biso min: 3.66 Å2
Refinement stepCycle: LAST / Resolution: 1.28→34.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 25 357 1622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071336
X-RAY DIFFRACTIONf_angle_d1.4471802
X-RAY DIFFRACTIONf_chiral_restr0.084194
X-RAY DIFFRACTIONf_plane_restr0.005231
X-RAY DIFFRACTIONf_dihedral_angle_d11.087501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.28-1.30.2581030.23681592169552
1.3-1.32130.295890.22041823191259
1.3213-1.34410.2501880.21312060214866
1.3441-1.36860.22721310.192325245674
1.3686-1.39490.21421340.17442521265581
1.3949-1.42340.19841430.15892674281787
1.4234-1.45430.18741430.14612761290489
1.4543-1.48810.2241510.13692822297392
1.4881-1.52540.14911480.11722929307794
1.5254-1.56660.15891850.10932932311796
1.5666-1.61270.15391630.10642957312096
1.6127-1.66480.16031370.10792964310196
1.6648-1.72430.16241700.10352960313095
1.7243-1.79330.14581710.10922938310996
1.7933-1.87490.16791660.10272894306095
1.8749-1.97370.13221490.09522966311595
1.9737-2.09740.14641750.09472885306094
2.0974-2.25930.14911220.09692928305094
2.2593-2.48660.14191370.10972958309594
2.4866-2.84630.13911490.12422865301493
2.8463-3.58540.13671450.1092877302293
3.5854-34.7940.13531470.12432780292790

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