3S67

Crystal structure of V57P mutant of human cystatin C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein.

Orlikowska, M., Szymanska, A., Borek, D., Otwinowski, Z., Skowron, P., Jankowska, E.

(2013) Acta Crystallogr D Biol Crystallogr 69: 577-586

  • DOI: 10.1107/S0907444912051657
  • Primary Citation of Related Structures:  
    3S67, 3SVA

  • PubMed Abstract: 

    • Wild-type human cystatin C (hCC wt) is a low-molecular-mass protein (120 amino-acid residues, 13,343 Da) that is found in all nucleated cells. Physiologically, it functions as a potent regulator of cysteine protease activity. While the biologically active hCC wt is a monomeric protein, all crystallization efforts to date have resulted in a three-dimensional domain-swapped dimeric structure ...

    Wild-type human cystatin C (hCC wt) is a low-molecular-mass protein (120 amino-acid residues, 13,343 Da) that is found in all nucleated cells. Physiologically, it functions as a potent regulator of cysteine protease activity. While the biologically active hCC wt is a monomeric protein, all crystallization efforts to date have resulted in a three-dimensional domain-swapped dimeric structure. In the recently published structure of a mutated hCC, the monomeric fold was preserved by a stabilization of the conformationally constrained loop L1 caused by a single amino-acid substitution: Val57Asn. Additional hCC mutants were obtained in order to elucidate the relationship between the stability of the L1 loop and the propensity of human cystatin C to dimerize. In one mutant Val57 was substituted by an aspartic acid residue, which is favoured in β-turns, and in the second mutant proline, a residue known for broadening turns, was substituted for the same Val57. Here, 2.26 and 3.0 Å resolution crystal structures of the V57D andV57P mutants of hCC are reported and their dimeric architecture is discussed in terms of the stabilization and destabilization effects of the introduced mutations.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystatin-CA120Homo sapiensMutation(s): 1 
Gene Names: CST3
UniProt & NIH Common Fund Data Resources
Find proteins for P01034 (Homo sapiens)
Explore P01034 
Go to UniProtKB:  P01034
PHAROS:  P01034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01034
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.135α = 90
b = 140.135β = 90
c = 140.135γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Derived calculations
  • Version 1.2: 2013-04-03
    Changes: Database references