1G96

HUMAN CYSTATIN C; DIMERIC FORM WITH 3D DOMAIN SWAPPING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping.

Janowski, R.Kozak, M.Jankowska, E.Grzonka, Z.Grubb, A.Abrahamson, M.Jaskolski, M.

(2001) Nat Struct Biol 8: 316-320

  • DOI: https://doi.org/10.1038/86188
  • Primary Citation of Related Structures:  
    1G96

  • PubMed Abstract: 

    The crystal structure of human cystatin C, a protein with amyloidogenic properties and a potent inhibitor of cysteine proteases, reveals how the protein refolds to produce very tight two-fold symmetric dimers while retaining the secondary structure of the monomeric form. The dimerization occurs through three-dimensional domain swapping, a mechanism for forming oligomeric proteins. The reconstituted monomer-like domains are similar to chicken cystatin except for one inhibitory loop that unfolds to form the 'open interface' of the dimer. The structure explains the tendency of human cystatin C to dimerize and suggests a mechanism for its aggregation in the brain arteries of elderly people with amyloid angiopathy. A more severe 'conformational disease' is associated with the L68Q mutant of human cystatin C, which causes massive amyloidosis, cerebral hemorrhage and death in young adults. The structure of the three-dimensional domain-swapped dimers shows how the L68Q mutation destabilizes the monomers and makes the partially unfolded intermediate less unstable. Higher aggregates may arise through the three-dimensional domain-swapping mechanism occurring in an open-ended fashion in which partially unfolded molecules are linked into infinite chains.


  • Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYSTATIN C120Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01034 (Homo sapiens)
Explore P01034 
Go to UniProtKB:  P01034
GTEx:  ENSG00000101439 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01034
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.216 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.53α = 90
b = 140.53β = 90
c = 140.53γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description