1G96

HUMAN CYSTATIN C; DIMERIC FORM WITH 3D DOMAIN SWAPPING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 

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.Mol.Biol. 8: 316-320

  • DOI: 10.1038/86188

  • 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: 
    • 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
    • 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.,Sect.D 55: 1939
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYSTATIN C
A
120Homo sapiensMutation(s): 0 
Gene Names: CST3
Find proteins for P01034 (Homo sapiens)
Go to Gene View: CST3
Go to UniProtKB:  P01034
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 140.530α = 90.00
b = 140.530β = 90.00
c = 140.530γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model