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- PDB-3rd9: Human Cyclophilin D Complexed with a Fragment -

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Basic information

Entry
Database: PDB / ID: 3rd9
TitleHuman Cyclophilin D Complexed with a Fragment
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE/ISOMERASE INHIBITOR / beta barrel / prolyl cis/trans isomerase / mitochondria / 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-MSY / DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsColliandre, L. / Ahmed-Belkacem, H. / Bessin, Y. / Pawlotsky, J.M. / 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
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,2303
Polymers17,8701
Non-polymers3592
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.214, 57.214, 87.198
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-615-

HOH

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Components

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


Mass: 17870.400 Da / Num. of mol.: 1 / Fragment: UNP residues 43-207 / 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-MSY / 3-(3-methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl)benzenesulfonamide


Mass: 253.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11N3O3S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 100K, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→29.7 Å / Num. all: 27758 / Num. obs: 26731 / % possible obs: 96.3 % / Observed criterion σ(I): 29.4 / Redundancy: 7.1 % / Rsym value: 0.049
Reflection shellResolution: 1.4→1.436 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 8.4 / Rsym value: 0.081 / % possible all: 79.8

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Processing

Software
NameVersionClassification
DNAdata collection
X-PLORmodel building
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BIT

2bit


Resolution: 1.4→29.66 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.511 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14965 1414 5 %RANDOM
Rwork0.12169 ---
all0.123 27558 --
obs0.12306 26731 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 24 407 1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221334
X-RAY DIFFRACTIONr_bond_other_d0.0030.02920
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9711800
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0012252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5172455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09115233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.398156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
X-RAY DIFFRACTIONr_nbd_refined0.1840.2223
X-RAY DIFFRACTIONr_nbd_other0.1840.21017
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2666
X-RAY DIFFRACTIONr_nbtor_other0.0860.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1330.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.293
X-RAY DIFFRACTIONr_mcbond_it0.3821.51043
X-RAY DIFFRACTIONr_mcbond_other0.0931.5344
X-RAY DIFFRACTIONr_mcangle_it0.51321322
X-RAY DIFFRACTIONr_scbond_it0.8213612
X-RAY DIFFRACTIONr_scangle_it1.0524.5476
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.161 82 -
Rwork0.143 1491 -
obs--73.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6381-0.1924-0.14470.62990.01090.60570.01270.0598-0.0208-0.0564-0.01230.00510.0039-0.0045-0.0004-0.0528-0.0028-0.0043-0.04220.0025-0.04812.344114.033123.6715
247.10210.83268.9312.549713.818575.3092-0.28051.0953-0.3681-0.0406-0.53080.96740.59870.31240.81130.0030.00780.00790.0080.01180.00253.687718.182615.9095
3191.8365-1.66823.8342114.3139-121.0925149.6773-0.2030.73850.4624-0.2780.11180.7567-0.36940.04250.09120.0136-0.0039-0.00750.0092-0.00070.015718.958721.98656.0002
40.7913-0.1782-0.1680.75130.08740.69460.01010.0834-0.0118-0.0727-0.01310.01080.0097-0.020.0030.0363-0.008-0.00810.03890.00870.035412.407513.453922.8712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X44 - 207
2X-RAY DIFFRACTION2X301
3X-RAY DIFFRACTION3X302
4X-RAY DIFFRACTION4X401 - 807

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