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- PDB-9upi: Entamoeba histolytica Cyclophilin 18 in complex with Cyclosporin A -

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Basic information

Entry
Database: PDB / ID: 9upi
TitleEntamoeba histolytica Cyclophilin 18 in complex with Cyclosporin A
Components
  • Cyclosporin A (CsA)
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / cyclophilin / PPIase
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 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
ISOPROPYL ALCOHOL / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGandhi, S. / Vasudevan, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal structure of Entamoeba histolytica cyclophilin 18 in complex with Cyclosporin A
Authors: Gandhi, S. / Vasudevan, D.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: 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 (CsA)
D: Cyclosporin A (CsA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0907
Polymers40,9094
Non-polymers1803
Water3,603200
1
A: Peptidyl-prolyl cis-trans isomerase
C: Cyclosporin A (CsA)


Theoretical massNumber of molelcules
Total (without water)20,4552
Polymers20,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-7 kcal/mol
Surface area7670 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
D: Cyclosporin A (CsA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6355
Polymers20,4552
Non-polymers1803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.622, 85.826, 62.961
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19234.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Gene: EHI7A_066540 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: N9TCE9, peptidylprolyl isomerase
#2: Protein/peptide Cyclosporin A (CsA)


Mass: 1220.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tolypocladium inflatum (fungus)
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.01 % / Description: Rod shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.7→28.71 Å / Num. obs: 42507 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.998 / Net I/σ(I): 17.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2212 / CC1/2: 0.821 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→28.71 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1763 2122 5 %
Rwork0.1508 --
obs0.1521 42476 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 12 200 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092761
X-RAY DIFFRACTIONf_angle_d1.143727
X-RAY DIFFRACTIONf_dihedral_angle_d7.686382
X-RAY DIFFRACTIONf_chiral_restr0.067400
X-RAY DIFFRACTIONf_plane_restr0.008494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.23671570.18082646X-RAY DIFFRACTION100
1.74-1.780.17981320.1652671X-RAY DIFFRACTION100
1.78-1.830.1961300.15492679X-RAY DIFFRACTION100
1.83-1.890.19371380.15022722X-RAY DIFFRACTION100
1.89-1.950.16661400.14182643X-RAY DIFFRACTION100
1.95-2.020.19051450.1372689X-RAY DIFFRACTION100
2.02-2.10.1591470.13632704X-RAY DIFFRACTION100
2.1-2.190.18651670.13412660X-RAY DIFFRACTION100
2.19-2.310.16911460.13662665X-RAY DIFFRACTION100
2.31-2.450.1751400.13652688X-RAY DIFFRACTION100
2.45-2.640.1681200.14522708X-RAY DIFFRACTION100
2.64-2.910.19121230.15462744X-RAY DIFFRACTION100
2.91-3.330.17641520.15622693X-RAY DIFFRACTION100
3.33-4.190.15381280.15322724X-RAY DIFFRACTION100
4.19-28.710.17271570.17152718X-RAY DIFFRACTION99

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