3UL5

Saccharum officinarum canecystatin-1 in space group C2221


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

X-ray crystallography and NMR studies of domain-swapped canecystatin-1.

Valadares, N.F.de Oliveira-Silva, R.Cavini, I.A.Marques, I.A.Pereira, H.D.Soares-Costa, A.Henrique-Silva, F.Kalbitzer, H.R.Munte, C.E.Garratt, R.C.

(2013) FEBS J 280: 1028-1038

  • DOI: https://doi.org/10.1111/febs.12095
  • Primary Citation of Related Structures:  
    3UL5, 3UL6

  • PubMed Abstract: 

    The three-dimensional structure of canecystatin-1, a potent inhibitor of cysteine proteases from sugarcane (Saccharum officinarum), has been solved in two different crystal forms. In both cases, it is seen to exist as a domain-swapped dimer, the first such observation for a cystatin of plant origin. Size exclusion chromatography and multidimensional NMR spectroscopy show the dimer to be the dominant species in solution, despite the presence of a measurable quantity of monomer undergoing slow exchange. The latter is believed to be the active species, whereas the domain-swapped dimer is presumably inactive, as its first inhibitory loop has been extended to form part of a long β-strand that forms a double-helical coiled coil with its partner from the other monomer. A similar structure is observed in human cystatin C, but the spatial disposition of the two lobes of the dimer is rather different. Dimerization is presumably a mechanism by which canecystatin-1 can be kept inactive within the plant, avoiding the inhibition of endogenous proteases. The structure described here provides a platform for the rational design of specific cysteine protease inhibitors for biotechnological applications.


  • Organizational Affiliation

    Center for Structural Molecular Biotechnology, Department of Physics and Informatics, Physics Institute of São Carlos, University of São Paulo, São Carlos-SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Canecystatin-1
A, B, C, D
139Saccharum officinarumMutation(s): 0 
Gene Names: cystatin-1
UniProt
Find proteins for Q7Y0Q9 (Saccharum officinarum)
Explore Q7Y0Q9 
Go to UniProtKB:  Q7Y0Q9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Y0Q9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.768α = 90
b = 113.993β = 90
c = 86.776γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references, Refinement description
  • Version 1.2: 2013-05-22
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description