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- PDB-8r7u: Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii i... -

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Basic information

Entry
Database: PDB / ID: 8r7u
TitleCrystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with dihydro Cyclosporin A
Components
  • Dihydrocyclosporin A
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / CYCLOPHILIN COMPLEX / peptidylprolyl isomerase activity
Function / homology
Function and homology information


cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding / intracellular membrane-bounded organelle / 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
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-115331GB-I00 Spain
Citation
Journal: Protein Sci. / Year: 2024
Title: Evaluating the potential of non-immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies.
Authors: Favretto, F. / Jimenez-Faraco, E. / Catucci, G. / Di Matteo, A. / Travaglini-Allocatelli, C. / Sadeghi, S.J. / Dominici, P. / Hermoso, J.A. / Astegno, A.
#1: Journal: ACS Infect Dis / Year: 2023
Title: Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii in complex with Cyclosporin A at 1.1 Angstroms resolution
Authors: Jimenez-Faraco, E. / Hermoso, J.A.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Peptidyl-prolyl cis-trans isomerase
A: Peptidyl-prolyl cis-trans isomerase
C: Dihydrocyclosporin A
D: Dihydrocyclosporin A


Theoretical massNumber of molelcules
Total (without water)48,8324
Polymers48,8324
Non-polymers00
Water8,071448
1
B: Peptidyl-prolyl cis-trans isomerase
D: Dihydrocyclosporin A


Theoretical massNumber of molelcules
Total (without water)24,4162
Polymers24,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area9120 Å2
MethodPISA
2
A: Peptidyl-prolyl cis-trans isomerase
C: Dihydrocyclosporin A


Theoretical massNumber of molelcules
Total (without water)24,4162
Polymers24,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.346, 118.109, 47.460
Angle α, β, γ (deg.)90.000, 103.670, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 23193.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: There are two additional residues in N-term, that remain after the His tag cleavage and are not observed in density. Glycine (-1) Histidine (0)
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_026260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6KAD1, peptidylprolyl isomerase
#2: Protein/peptide Dihydrocyclosporin A


Type: Cyclic peptide / Class: Inhibitor / Mass: 1222.641 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Analogue of cyclosporine A. It is a cyclic undecapeptide. Cyclization is achieved by linking the N- and the C- termini.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002553
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) Dihydrocyclosporin A, is a derivative of cyclosporin A that is not immunosuppressive. It has been shown to inhibit growth of Leishmania donovani.
Has ligand of interestY
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M citric acid pH 3.5, and 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.2→42.96 Å / Num. obs: 125896 / % possible obs: 98.67 % / Redundancy: 6.8 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Net I/σ(I): 16.8
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 12366 / CC1/2: 0.752 / Rpim(I) all: 0.418 / % possible all: 97.04

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
PHENIX1.20.1refinement
XDS0.86data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→42.96 Å / SU ML: 0.1502 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 6379 5.07 %
Rwork0.1716 119462 -
obs0.1723 125841 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 170 448 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133352
X-RAY DIFFRACTIONf_angle_d1.52244548
X-RAY DIFFRACTIONf_chiral_restr0.0886486
X-RAY DIFFRACTIONf_plane_restr0.011595
X-RAY DIFFRACTIONf_dihedral_angle_d22.5863516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.37191920.37273942X-RAY DIFFRACTION96.86
1.21-1.230.35151900.35173872X-RAY DIFFRACTION97.11
1.23-1.240.3432140.32223940X-RAY DIFFRACTION97.15
1.24-1.260.2851820.30323901X-RAY DIFFRACTION97.24
1.26-1.280.28812000.28283987X-RAY DIFFRACTION97.3
1.28-1.290.29411940.26513928X-RAY DIFFRACTION97.75
1.29-1.310.24552550.24423894X-RAY DIFFRACTION97.67
1.31-1.330.252040.2273942X-RAY DIFFRACTION97.64
1.33-1.350.24742200.22143924X-RAY DIFFRACTION98.18
1.35-1.370.21762020.21313976X-RAY DIFFRACTION97.85
1.37-1.40.22812250.21053937X-RAY DIFFRACTION98.14
1.4-1.420.21752270.20563948X-RAY DIFFRACTION98.42
1.42-1.450.22242060.20763949X-RAY DIFFRACTION98.41
1.45-1.480.2242310.21413991X-RAY DIFFRACTION98.51
1.48-1.510.21462060.19583939X-RAY DIFFRACTION98.5
1.51-1.550.18712150.17713968X-RAY DIFFRACTION98.77
1.55-1.590.17852020.16984015X-RAY DIFFRACTION98.78
1.59-1.630.18952420.1633944X-RAY DIFFRACTION98.82
1.63-1.680.18552270.1624010X-RAY DIFFRACTION99.04
1.68-1.730.18272140.16474009X-RAY DIFFRACTION99.48
1.73-1.790.19172030.17114017X-RAY DIFFRACTION99.58
1.79-1.860.17722170.17063995X-RAY DIFFRACTION99.65
1.86-1.950.20792200.17144026X-RAY DIFFRACTION99.74
1.95-2.050.16262150.16744056X-RAY DIFFRACTION99.86
2.05-2.180.15732320.16224002X-RAY DIFFRACTION99.95
2.18-2.350.1752000.16934070X-RAY DIFFRACTION99.95
2.35-2.590.19952150.17444055X-RAY DIFFRACTION100
2.59-2.960.19972320.17544057X-RAY DIFFRACTION100
2.96-3.730.18251920.15414058X-RAY DIFFRACTION100
3.73-42.960.14192050.13364110X-RAY DIFFRACTION99.77
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)
10.971744818238-0.1884184271260.4575739398972.131891541480.1584434186431.19958687025-0.0620375757504-0.1262336464270.001185315132210.1913959431670.100720268075-0.1506623844910.00255025571334-0.0734285259362-0.02724205012040.09063680232160.0247883768107-0.01999597173830.114492304299-0.03654527919850.1221129881019.09275437196-20.861917039216.3629011466
21.579821577181.405852455950.2226389426913.806535899520.458326484070.7864739000530.146967819333-0.202534212967-0.02666359970420.224613665667-0.236502359104-0.107778855107-0.006244088703620.009206910416240.08020598707990.122260194124-0.0329085040828-0.02094455864940.1232852021310.04034950866150.1153418341460.0164069530185-55.65284462067.77444035449
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 13 - 301 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain B and resseq 13:301)BA - B
22(chain A and resseq 12:301)AC - D

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