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- PDB-2oju: X-ray structure of complex of human cyclophilin J with cyclosporin A -

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Basic information

Entry
Database: PDB / ID: 2oju
TitleX-ray structure of complex of human cyclophilin J with cyclosporin A
Components
  • CYCLOSPORIN ACiclosporin
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 3
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / protein folding / nucleoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-like / Cyclophilin / 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 ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase-like 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXia, Z. / Huang, L.
CitationJournal: To be Published
Title: Targeting Cyclophilin J, a Novel Peptidyl-Prolyl Isomerase, Can Induce Cellular G1/S Arrest and Repress the Growth of Hepatocellular Carcinoma
Authors: Chen, J. / Chen, S. / Huang, L. / Zhao, X. / Tan, J. / Huang, C. / Saiyin, H. / Zhang, M. / Zeng, X. / Xi, J. / Wan, B. / Zhao, Y. / Xia, Z. / Jiang, H. / Yi, Q. / Liu, J.O. / Yu, L.
History
DepositionJan 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 25, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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-LIKE 3
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 3
C: CYCLOSPORIN A
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)39,9424
Polymers39,9424
Non-polymers00
Water57632
1
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 3
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)19,9712
Polymers19,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7.3 kcal/mol
Surface area8710 Å2
MethodPISA
2
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 3
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)19,9712
Polymers19,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6.6 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.387, 64.387, 200.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 3 / PPIASE / ROTAMASE / CYCLOPHILIN-LIKE PROTEIN PPIL3 / CYCLOPHILIN J / CYPJ


Mass: 18750.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: FETAL BRAIN / Gene: PPIL3B / Plasmid: PTXB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9H2H8, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / Ciclosporin / CICLOSPORIN / CICLOSPORINE / Ciclosporin


Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / 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.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
Sequence detailsTHE N-TERMINAL 6 RESIDUES 'SRVDGG' IN CHAINS A AND B IS AN ENGINEERED EXPRESSION TAG

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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: 3.04 Å3/Da / Density % sol: 59.63 %
Crystal growpH: 7.4
Details: 0.1MOL/L TRIS-HCL(PH=7.4), 6%(V/V) DMSO, 18%(W/V) PEG8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9826
DetectorDetector: CCD / Date: Feb 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9826 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19272 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.406 / % possible all: 83.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OK3

2ok3


Resolution: 2.4→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 220039.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1793 9.7 %RANDOM
Rwork0.193 ---
obs0.193 18460 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.27 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å21.34 Å20 Å2
2---2.47 Å20 Å2
3---4.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 0 32 2794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.429 135 9.6 %
Rwork0.359 1264 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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