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 1.3 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: 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 o ...

    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.


    Related Citations: 
    • Expression of selenomethionyl derivative and preliminary crystallographic studies of human cystatin C
      Kozak, M., Jankowska, E., Janowski, R., Grzonka, Z., Grubb, A., Alvarez Fernandez, M., Abrahamson, M., Jaskolski, M.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1939
    • The 2.0 angstrom X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteases
      Bode, W., Engh, R., Musil, D., Thiele, U., Huber, R., Karshikov, A., Brzin, J., Kos, J., Turk, V.
      (1988) EMBO J 7: 2593
    • NMR structural studies of human cystatin C dimers and monomers
      Ekiel, I., Abrahamson, M., Fulton, D.B., Lindahl, P., Storer, A.C., Levadoux, W., Lafrance, M., Labelle, S., Pomerleau, Y., Groleau, D., LeSauter, L., Gehring, K.
      (1997) J Mol Biol 271: 266

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYSTATIN CA120Homo sapiensMutation(s): 0 
Gene Names: CST3
Find proteins for P01034 (Homo sapiens)
Explore P01034 
Go to UniProtKB:  P01034
NIH Common Fund Data Resources
PHAROS  P01034
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 

  • 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