1CWB

THE X-RAY STRUCTURE OF (MEBM2T)1-CYCLOSPORIN COMPLEXED WITH CYCLOPHILIN A PROVIDES AN EXPLANATION FOR ITS ANOMALOUSLY HIGH IMMUNOSUPPRESSIVE ACTIVITY

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

The X-Ray Structure of (Mebm2T)1-Cyclosporin Complexed with Cyclophilin a Provides an Explanation for its Anomalously High Immunosuppressive Activity.

Mikol, V., Kallen, J., Walkinshaw, M.D.

(1994) Protein Eng 7: 597

  • DOI: 10.1093/protein/7.5.597
  • Primary Citation of Related Structures:  
    1CWB

  • PubMed Abstract: 

    • For most of the cyclosporin A (CsA) analogs, there is generally a good correlation between cyclophilin binding and immunosuppression. However, this relationship does not seem to hold for 4-[(E)-2-butenyl]-4,4,N-trimethyl-L-threonine1 (MeBm2t)1-CsA. Its affinity for cyclophilin was reported to be approximately 1% that of CsA and its immunosuppressive activity in vitro was shown to be approximately 30% that of CsA ...

    For most of the cyclosporin A (CsA) analogs, there is generally a good correlation between cyclophilin binding and immunosuppression. However, this relationship does not seem to hold for 4-[(E)-2-butenyl]-4,4,N-trimethyl-L-threonine1 (MeBm2t)1-CsA. Its affinity for cyclophilin was reported to be approximately 1% that of CsA and its immunosuppressive activity in vitro was shown to be approximately 30% that of CsA. We report here the crystal structure of a complex between recombinant human cyclophilin A (CypA) and (MeBm2t)1-CsA which has been determined by X-ray crystallography at 2.2 A resolution and refined to an R-factor of 16.3%. (MeBm2t)1-CsA shows a similar bound conformation and network of interactions to CypA as CsA. The measured lower affinity for CypA cannot therefore be explained by a different mode of binding. We propose that the poor affinity to CypA could be accounted for by the existence of an equilibrium in aqueous solution between a 'cyclophilin bound conformation' and a 'non-binding conformation' of (MeBm2t)1-CsA. The relatively high immunosuppressive activity is suggested to result from slight conformational differences observed in the effector domain.

    Related Citations: 
    • Crystallization of the Complex between Cyclophilin a and Cyclosporin Derivatives: The Use of Cross- Seeding.
      Mikol, V., Duc, D.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 543
    • Improved Binding Affinity for Cyclophilin a by a Cyclosporin Derivative Singly Modified at its Effector Domain.
      Papageorgiou, C., Florineth, A., Mikol, V.
      (1994) J Med Chem 37: 3674
    • X-Ray Structure of a Monomeric Cyclophilin A- Cyclosporin a Crystal Complex at 2.1 A Resolution.
      Mikol, V., Kallen, J., Pflugl, G., Walkinshaw, M.D.
      (1993) J Mol Biol 234: 1119
    • X-Ray Structure of a Decameric Cyclophilin- Cyclosporin Crystal Complex.
      Pflugl, G., Kallen, J., Schirmer, T., Jansonius, J.N., Zurini, M.G., Walkinshaw, M.D.
      (1993) Nature 361: 91
    Organizational Affiliation: 

    Sandoz AG, Basle, Switzerland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE AA165Homo sapiensMutation(s): 0 
Gene Names: CYCLOPHILIN, PPIA, CYPA
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOSPORIN AB [auth C]11Tolypocladium inflatumMutation(s): 1 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA		B [auth C]L-PEPTIDE LINKINGC4 H9 N O2ALA
MLE
Query on MLE		B [auth C]L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA		B [auth C]L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR		B [auth C]PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000765
Query on PRD_000765		B [auth C]CYCLOSPORIN A, 5 mutationCyclic peptide /  Immunosuppressant Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.869α = 90
b = 61.292β = 90
c = 71.993γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other