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- PDB-1cyn: CYCLOPHILIN B COMPLEXED WITH [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN -

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Basic information

Entry
Database: PDB / ID: 1cyn
TitleCYCLOPHILIN B COMPLEXED WITH [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOSPORIN / ISOMERASE / ROTAMASE
Function / homology
Function and homology information


endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / protein peptidyl-prolyl isomerization / smooth endoplasmic reticulum / chaperone-mediated protein folding ...endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / protein peptidyl-prolyl isomerization / smooth endoplasmic reticulum / chaperone-mediated protein folding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / neutrophil chemotaxis / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / bone development / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / melanosome / protein folding / protein stabilization / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / 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
[D-(CHOLINYLESTER)SER8]-CYCLOSPORIN / : / Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsMikol, V. / Kallen, J. / Walkinshaw, M.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: X-Ray Structure of a Cyclophilin B/Cyclosporin Complex: Comparison with Cyclophilin a and Delineation of its Calcineurin-Binding Domain.
Authors: Mikol, V. / Kallen, J. / Walkinshaw, M.D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: X-Ray Structure of a Monomeric Cyclophilin A- Cyclosporin a Crystal Complex at 2.1 A Resolution.
Authors: Mikol, V. / Kallen, J. / Pflugl, G. / Walkinshaw, M.D.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: A Novel Secreted Cyclophilin-Like Protein (Scylp)
Authors: Spik, G. / Haendler, B. / Delemas, O. / Mariller, C. / Chamoux, M. / Maes, P. / Tartar, A. / Montreuil, J. / Stedman, K. / Kocher, H.P. / Keller, R. / Hiestand, P.C. / Movva, R.
History
DepositionMay 22, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: 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 1.5Sep 12, 2018Group: Data collection / Other / Structure summary
Category: pdbx_database_status / pdbx_molecule / pdbx_molecule_features
Item: _pdbx_database_status.process_site / _pdbx_molecule.prd_id ..._pdbx_database_status.process_site / _pdbx_molecule.prd_id / _pdbx_molecule_features.details / _pdbx_molecule_features.name / _pdbx_molecule_features.prd_id
Revision 1.6Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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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
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,9292
Polymers20,9292
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-8 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.460, 46.944, 115.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B / PPIASE B / ROTAMASE B / CYCLOPHILIN B


Mass: 19692.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CYCLOPHILIN / Gene (production host): CYCLOPHILIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23284, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / CYCLOSPORINE / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1236.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D-(CHOLINYL)SER AT POSITION 1 / Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus)
References: NOR: NOR00033, [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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 protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1drop
29.75 %(w/v)PEG80001drop
32.5 %dimethyl sulfoxide1drop
40.02 %1dropNaN3
50.5 mMcyclophilin B1drop
60.5 mM[CES8]CsA1drop
7100 mMTris-HCl1reservoir
819.5 %(w/v)PEG80001reservoir
95 %(v/v)dimethyl sulfoxide1reservoir
100.04 %1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 15219 / % possible obs: 84.1 % / Observed criterion σ(I): 2
Reflection
*PLUS
Num. measured all: 56456 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.97 Å / % possible obs: 52 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.85→8 Å / σ(F): 2
Details: THE FIRST SIX RESIDUES AT THE N- TERMINUS WERE CLEAVED OFF DURING THE ISOLATION OF THE PROTEIN AS CONFIRMED BY SEQUENCE ANALYSIS OF DISSOLVED CRYSTALS. THE CHOLINYL DERIVATIZATION IN ...Details: THE FIRST SIX RESIDUES AT THE N- TERMINUS WERE CLEAVED OFF DURING THE ISOLATION OF THE PROTEIN AS CONFIRMED BY SEQUENCE ANALYSIS OF DISSOLVED CRYSTALS. THE CHOLINYL DERIVATIZATION IN POSITION 8 OF CYCLOSPORIN WAS NOT DETECTABLE BEYOND THE C-BETA IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection
Rwork0.16 -
obs0.16 15028
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 196 1670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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