Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.27 kDa 
• Atom Count: 1483 
• Residue Count: 176 
• Unique protein chains: 2

1CWB

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

• DOI: 10.2210/pdb1CWB/pdb

• Classification: ISOMERASE/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens, Tolypocladium inflatum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1995-09-06 Released: 1996-01-29 
• Deposition Author(s): Mikol, V., Kallen, J., Walkinshaw, M.D.

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Experimental Data Snapshot

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

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

• PubMed: 8073029 
• 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. 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.

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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

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Organizational Affiliation: 

Sandoz AG, Basle, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	A	165	Homo sapiens	Mutation(s): 0  Gene Names: CYCLOPHILIN, PPIA, CYPA EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937 GTEx  ENSG00000196262

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	C	11	Tolypocladium inflatum	Mutation(s): 1

Small Molecules

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	C	L-PEPTIDE LINKING	C4 H9 N O2		ALA
MLE	C	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	C	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000765	C	CYCLOSPORIN A, 5 mutation	Cyclic peptide /  Immunosuppressant		--

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 = 36.869	α = 90
b = 61.292	β = 90
c = 71.993	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-09-06 
• Released Date: 1996-01-29 
Deposition Author(s): Mikol, V., Kallen, J., Walkinshaw, M.D.

Revision History 

• 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