5ZC1

X-ray diffraction analysis of the CsStefin-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 

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Literature

Structural basis of the cystein protease inhibitor Clonorchis sinensis Stefin-1.

Park, S.Y.Jeong, M.S.Park, S.A.Ha, S.C.Na, B.K.Jang, S.B.

(2018) Biochem Biophys Res Commun 498: 9-17

  • DOI: 10.1016/j.bbrc.2018.02.196
  • Primary Citation of Related Structures:  
    5ZC1

  • PubMed Abstract: 
  • Cystein protease plays a critical role as a virulence factor in the development and progression of various diseases. Cystatin is a superfamily of cysteine protease inhibitors that participates in various physiological and pathological processes. The cysteine protease inhibitor CsStein-1 isolated from Clonorchis sinensis belongs to the type 1 stefin of cystatins ...

    Cystein protease plays a critical role as a virulence factor in the development and progression of various diseases. Cystatin is a superfamily of cysteine protease inhibitors that participates in various physiological and pathological processes. The cysteine protease inhibitor CsStein-1 isolated from Clonorchis sinensis belongs to the type 1 stefin of cystatins. This inhibitor regulates the activity and processing of CsCF (Cathepsin F of Clonorchis sienesis), which plays an important role in parasite nutrition and host-parasite interaction. CsStefin-1 has also been proposed as a host immune modulator and a participant in the mechanism associated with anti-inflammatory ability. Here, we report the first crystal structure of CsStefin-1 determined by the multi-wavelength anomalous diffraction (MAD) method to 2.3 Å. There are six molecules of CsStefin-1 per asymmetric unit, with a solvent content of 36.5%. The structure of CsStefin-1 is composed of twisted four-stranded antiparallel β-sheets, a central α-helix, and a short α-helix. We also demonstrate that CsStefin-1 binds to CsCF-8 cysteine protease and inhibits its activity. In addition, a molecular docking model of CsStefin-1 and CsCF-8 was developed using homology modeling based on their structures. The structural information regarding CsStefin-1 and molecular insight into its interaction with CsCF-8 are important to understanding their biological function and to design of inhibitors that modulate cysteine protease activity.


    Organizational Affiliation

    Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan, 46241, Republic of Korea. Electronic address: sbjang@pusan.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystatin-1A, B, C, D, E, F136Clonorchis sinensisMutation(s): 0 
UniProt
Find proteins for A6YID9 (Clonorchis sinensis)
Explore A6YID9 
Go to UniProtKB:  A6YID9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.45α = 90
b = 56.996β = 99.06
c = 101.134γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-14 
  • Released Date: 2018-12-26 
  • Deposition Author(s): Jang, S.B., Park, S.Y.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2015R1D1A1A01059594

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release