5YB9 | pdb_00005yb9

Crystal structure of a dimeric cyclophilin A from T.vaginalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.286 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5YB9

This is version 1.2 of the entry. See complete history

Literature

Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis

Martin, T.Lou, Y.C.Chou, C.C.Wei, S.Y.Sadotra, S.Cho, C.C.Lin, M.H.Tai, J.H.Hsu, C.H.Chen, C.

(2018) Sci Rep 8: 5410-5410

  • DOI: https://doi.org/10.1038/s41598-018-23821-5
  • Primary Citation Related Structures: 
    5YB9, 5YBA

  • PubMed Abstract: 

    Cyclophilin 1 (TvCyP1), a cyclophilin type peptidyl-prolyl isomerase present in the human parasite Trichomonas vaginalis, interacts with Myb1 and assists in its nuclear translocation. Myb1 regulates the expression of ap65-1 gene that encodes for a disease causing cytoadherence enzyme. Here, we determined the crystal structures of TvCyP1 and its complex with the minimum TvCyP1-binding sequence of Myb1 (Myb1 104-111 ), where TvCyP1 formed a homodimer, unlike other single domain cyclophilins. In the complex structure, one Myb1 104-111 peptide was bound to each TvCyP1 protomer, with G106-P107 and Y105 fitting well into the active site and auxiliary S2 pocket, respectively. NMR data further showed that TvCyP1 can catalyze the cis/trans isomerization of P107 in Myb1 104-111 . Interestingly, in the well-folded Myb1 protein (Myb1 35-141 ), the minimum binding sequence adopted a different conformation from that of unstructured Myb1 104-111 peptide, that could make P107 binding to the active site of TvCyP1 difficult. However, NMR studies showed that similar to Myb1 104-111 peptide, Myb1 35-141 also interacted with the active site of TvCyP1 and the dynamics of the Myb1 35-141 residues near P107 was reduced upon interaction. Together, the structure of TvCyP1 and detailed structural insights on TvCyP1-Myb1 interaction provided here could pave the way for newer drugs to treat drug-resistant strains.


  • Organizational Affiliation
    • Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 19.36 kDa 
  • Atom Count: 1,378 
  • Modeled Residue Count: 172 
  • Deposited Residue Count: 175 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase175Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_004440
EC: 5.2.1.8
UniProt
Find proteins for A2DT06 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
Explore A2DT06 
Go to UniProtKB:  A2DT06
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2DT06
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.286 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.505α = 90
b = 38.505β = 90
c = 365.697γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description