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- PDB-8r7s: Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii i... -

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Basic information

Entry
Database: PDB / ID: 8r7s
TitleCrystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with NIM811 (N-methyl-4-isoleucine cyclosporin)
Components
  • CYCLOSPORIN A, 8 mutation
  • 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
CYCLOSPORIN A, 8 mutation / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 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
Authors: Favretto, F. / Jimenez-Faraco, E. / Conter, C. / Dominici, P. / Hermoso, J.A. / Astegno, 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
A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
C: CYCLOSPORIN A, 8 mutation
D: CYCLOSPORIN A, 8 mutation


Theoretical massNumber of molelcules
Total (without water)48,8284
Polymers48,8284
Non-polymers00
Water9,638535
1
A: Peptidyl-prolyl cis-trans isomerase
D: CYCLOSPORIN A, 8 mutation


Theoretical massNumber of molelcules
Total (without water)24,4142
Polymers24,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area9120 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
C: CYCLOSPORIN A, 8 mutation


Theoretical massNumber of molelcules
Total (without water)24,4142
Polymers24,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.095, 118.187, 45.885
Angle α, β, γ (deg.)90.000, 103.270, 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 CYCLOSPORIN A, 8 mutation


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. THE CYCLOSPORIN A MOLECULE WAS MODIFIED AT POSITION 8 TO BE N-METHYL-ISOLEUCINE
Source: (synth.) synthetic construct (others) / References: CYCLOSPORIN A, 8 mutation
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
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: 2.1 Å3/Da / Density % sol: 40.74 % / Description: 41.42
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: 0.979264 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 1.17→44.66 Å / Num. obs: 132383 / % possible obs: 99.25 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Net I/σ(I): 14.33
Reflection shellResolution: 1.17→1.212 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 12900 / CC1/2: 0.807 / Rpim(I) all: 0.331 / % possible all: 97.78

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
REFMAC5.8.0405refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→44.66 Å / SU ML: 0.1022 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.6118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 6513 4.92 %RANDOM SELECTION
Rwork0.1482 125870 --
obs0.1492 132383 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.12 Å2
Refinement stepCycle: LAST / Resolution: 1.17→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 170 535 3797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01813396
X-RAY DIFFRACTIONf_angle_d1.67114614
X-RAY DIFFRACTIONf_chiral_restr0.1085494
X-RAY DIFFRACTIONf_plane_restr0.013607
X-RAY DIFFRACTIONf_dihedral_angle_d24.2294526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.180.22532040.2294087X-RAY DIFFRACTION96.34
1.18-1.190.23032080.21864146X-RAY DIFFRACTION97.84
1.19-1.210.20292170.21624140X-RAY DIFFRACTION98.53
1.21-1.220.22372200.20454169X-RAY DIFFRACTION98.61
1.22-1.240.22442040.20344164X-RAY DIFFRACTION98.56
1.24-1.260.23022170.1974119X-RAY DIFFRACTION98.66
1.26-1.280.20032380.19564223X-RAY DIFFRACTION99.05
1.28-1.290.20242260.1974119X-RAY DIFFRACTION98.95
1.29-1.310.20592080.18664249X-RAY DIFFRACTION99
1.31-1.340.19792020.18184116X-RAY DIFFRACTION99.31
1.34-1.360.21552270.17824212X-RAY DIFFRACTION99.2
1.36-1.380.17662340.17294168X-RAY DIFFRACTION99.48
1.38-1.410.1932210.16874241X-RAY DIFFRACTION99.29
1.41-1.440.17542320.16754153X-RAY DIFFRACTION99.41
1.44-1.470.19252240.16044200X-RAY DIFFRACTION99.51
1.47-1.50.17632140.15434179X-RAY DIFFRACTION99.34
1.5-1.540.17652110.15274216X-RAY DIFFRACTION99.64
1.54-1.580.17022450.15134217X-RAY DIFFRACTION99.64
1.58-1.630.17022100.1474162X-RAY DIFFRACTION99.54
1.63-1.680.15052210.14424228X-RAY DIFFRACTION99.78
1.68-1.740.15122150.14644241X-RAY DIFFRACTION99.82
1.74-1.810.18071900.14594258X-RAY DIFFRACTION99.89
1.81-1.90.16042210.1444205X-RAY DIFFRACTION99.66
1.9-20.1542200.14264229X-RAY DIFFRACTION99.6
2-2.120.16392040.13844216X-RAY DIFFRACTION99.71
2.12-2.280.15452050.13894240X-RAY DIFFRACTION99.71
2.28-2.510.16552040.15054213X-RAY DIFFRACTION99.35
2.51-2.880.17482150.14614252X-RAY DIFFRACTION99.64
2.88-3.630.16112270.13064221X-RAY DIFFRACTION99.87
3.63-44.660.14382290.12314287X-RAY DIFFRACTION99.93
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)
10.700742891688-0.27343377740.1245371802371.60470040605-0.07716718452570.508295076664-0.001894989822820.02690173420410.0284981968836-0.00405714533257-0.02526994078050.01020942803-0.00923149128938-0.0336123937680.0233411072830.0787732867397-0.003893409082480.03141299605210.148215381762-0.005336343843250.051239259683113.70323.31814.84
20.576673323304-0.1726678222030.1308034165511.96297325483-0.04992425507020.710615714851-0.005225402635570.011332864076-0.0436849786354-0.1576231964470.05349035786810.09171755152210.002092687973740.0471290082811-0.04293561337010.0852642775991-0.01155793937790.01102190121070.1377873232150.009192949676860.06322901968044.63457.7386.059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:211 ) OR ( CHAIN D AND RESID 1:11 )A12 - 211
2X-RAY DIFFRACTION1( CHAIN A AND RESID 12:211 ) OR ( CHAIN D AND RESID 1:11 )D1 - 11
3X-RAY DIFFRACTION2( CHAIN B AND RESID 12:211 ) OR ( CHAIN C AND RESID 1:11 )B12 - 211
4X-RAY DIFFRACTION2( CHAIN B AND RESID 12:211 ) OR ( CHAIN C AND RESID 1:11 )C1 - 11

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