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- PDB-4j5b: Human Cyclophilin D Complexed with an Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4j5b
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-6B4 / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Isomorphous Replacement / Resolution: 2.01 Å
AuthorsGelin, M. / Colliandre, L. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,0512
Polymers17,6521
Non-polymers3991
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.818, 57.818, 88.755
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


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-6B4 / 1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea


Mass: 398.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2010
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.01→30.069 Å / Num. all: 10246 / Num. obs: 10246 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.01-2.1240.2852.4547113720.28590.7
2.12-2.254.40.2033.3617714090.203100
2.25-2.44.30.1514.5583613530.15199.9
2.4-2.594.30.1225.7535812360.12299.7
2.59-2.844.30.0798.9488411470.07999.1
2.84-3.184.20.05213.7446210560.05298.5
3.18-3.674.20.03320.938299210.03397.5
3.67-4.4940.02228.931277800.02295.7
4.49-6.363.90.02126.323926110.02193.7
6.36-30.0693.50.01924.712653610.01990

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: Isomorphous Replacement / Resolution: 2.01→27.488 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.17 / σ(F): 1.16 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 483 4.8 %RANDOM
Rwork0.1557 ---
obs0.1571 10246 89.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.52 Å2 / Biso mean: 19.216 Å2 / Biso min: 4.66 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 28 84 1344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071300
X-RAY DIFFRACTIONf_angle_d1.2151755
X-RAY DIFFRACTIONf_chiral_restr0.072190
X-RAY DIFFRACTIONf_plane_restr0.004228
X-RAY DIFFRACTIONf_dihedral_angle_d12.979471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.13840.25371650.22612667283289
2.1384-2.30340.22291280.18012893302195
2.3034-2.53510.18841300.17762837296793
2.5351-2.90160.23391450.16472738288391
2.9016-3.65430.14371240.13542665278988
3.6543-27.4880.14481310.12372529266084
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)
11.0499-0.21940.15290.6867-0.08210.67170.05980.0992-0.0384-0.0555-0.03490.0701-0.01450.01440.05110.02580.00160.00270.0701-0.00630.046510.549314.544225.7011
20.183-0.0531-0.09510.2639-0.05470.09120.03120.0477-0.0047-0.014-0.02050.05010.10550.01850.00010.1044-0.00090.00120.157-0.00070.107512.559515.423627.3152
30.04750.0566-0.04220.0738-0.05360.04210.03030.08020.0240.00530.0784-0.0204-0.05670.1025-0.00030.3430.0486-0.030.4886-0.04030.36894.444120.163418.3347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:165 )A44 - 165
2X-RAY DIFFRACTION2( CHAIN A AND RESID 401:484 )A401 - 484
3X-RAY DIFFRACTION3( CHAIN A AND RESID 301:301 )A301

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