1YND

Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6 A resolution.

Kallen, J.Sedrani, R.Zenke, G.Wagner, J.

(2005) J.Biol.Chem. 280: 21965-21971

  • DOI: 10.1074/jbc.M501623200

  • PubMed Abstract: 
  • Sanglifehrin A (SFA) is a novel immunosuppressant isolated from Streptomyces sp. that binds strongly to the human immunophilin cyclophilin A (CypA). SFA exerts its immunosuppressive activity through a mode of action different from that of all other k ...

    Sanglifehrin A (SFA) is a novel immunosuppressant isolated from Streptomyces sp. that binds strongly to the human immunophilin cyclophilin A (CypA). SFA exerts its immunosuppressive activity through a mode of action different from that of all other known immunophilin-binding substances, namely cyclosporine A (CsA), FK506, and rapamycin. We have determined the crystal structure of human CypA in complex with SFA at 1.6 A resolution. The high resolution of the structure revealed the absolute configuration at all 17 chiral centers of SFA as well as the details of the CypA/SFA interactions. In particular, it was shown that the 22-membered macrocycle of SFA is deeply embedded in the same binding site as CsA and forms six direct hydrogen bonds with CypA. The effector domain of SFA, on the other hand, has a chemical and three-dimensional structure very different from CsA, already strongly suggesting different immunosuppressive mechanisms. Furthermore, two CypA.SFA complexes form a dimer in the crystal as well as in solution as shown by light scattering and size exclusion chromatography experiments. This observation raises the possibility that the dimer of CypA.SFA complexes is the molecular species mediating the immunosuppressive effect.


    Related Citations: 
    • Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure, and Binding Data
      Sedrani, R.,Kallen, J.,Cabrejas, L.M.,Papageorgiou, C.D.,Senia, F.,Rohrbach, S.,Wagner, D.,Thai, B.,Jutzi-Erne, A.M.,France, J.
      (2003) J.Am.Chem.Soc. 125: 3849


    Organizational Affiliation

    Protein Structure Unit, Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. joerg.kallen@pharma.novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase A
A, B
165Homo sapiensGene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFA
Query on SFA

Download SDF File 
Download CCD File 
A, B
SANGLIFEHRIN A
(3S,6S,9R,10R,11S,12S,13E,15E,18S,21S)-18-{(1E,3E,7S,8S)-9-[(2S,3R,4S,5S,6R,9S,11S)-9-ETHYL-4-HYDROXY-3,5,11-TRIMETHYL-8-OXO-1-OXA-7-AZASPIRO[5.5]UNDEC-2-YL]-8-HYDROXY-1,7-DIMETHYLNONA-1,3-DIENYL}-10,12-DIHYDROXY-3-(3-HYDROXYBENZYL)-6-ISOPROPYL-11-METHYL-9-(3-OXOBUTYL)-19-OXA-1,4,7,25-TETRAAZABICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20-TETRONE
C60 H91 N5 O13
ONJZYZYZIKTIEG-CFBQITSMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SFAIC50: 6.9 nM BINDINGMOAD
SFAIC50: 3.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.600α = 90.00
b = 65.400β = 90.00
c = 76.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance