1G96 | pdb_00001g96

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 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1G96

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 13.49 kDa 
  • Atom Count: 900 
  • Modeled Residue Count: 111 
  • Deposited Residue Count: 120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
PHAROS:  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 (Depositor) 
  • R-Value Work:  0.220 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
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

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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
  • Version 1.5: 2024-11-20
    Changes: Structure summary