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PDBsum entry 1r4c

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protein Protein-protein interface(s) links
Hydrolase inhibitor PDB id
1r4c
Jmol
Contents
Protein chains
(+ 2 more) 110 a.a. *
Waters ×205
* Residue conservation analysis
PDB id:
1r4c
Name: Hydrolase inhibitor
Title: N-truncated human cystatin c; dimeric form with 3d domain sw
Structure: Cystatin c. Chain: a, b, c, d, e, f, g, h. Fragment: human cystatin c without 10 n-terminal residues. Synonym: neuroendocrine basic polypeptide, gamma-trace, pos globulin. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cst3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.18Å     R-factor:   0.220     R-free:   0.259
Authors: R.Janowski,M.Abrahamson,A.Grubb,M.Jaskolski
Key ref:
R.Janowski et al. (2004). Domain swapping in N-truncated human cystatin C. J Mol Biol, 341, 151-160. PubMed id: 15312769 DOI: 10.1016/j.jmb.2004.06.013
Date:
06-Oct-03     Release date:   21-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01034  (CYTC_HUMAN) -  Cystatin-C
Seq:
Struc:
146 a.a.
110 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     defense response   10 terms 
  Biochemical function     protein binding     6 terms  

 

 
DOI no: 10.1016/j.jmb.2004.06.013 J Mol Biol 341:151-160 (2004)
PubMed id: 15312769  
 
 
Domain swapping in N-truncated human cystatin C.
R.Janowski, M.Abrahamson, A.Grubb, M.Jaskolski.
 
  ABSTRACT  
 
Human cystatin C (HCC) inhibits papain-like cysteine proteases by a binding epitope composed of two beta-hairpin loops and the N-terminal segment. HCC is found in all body fluids and is present at a particularly high level in the cerebrospinal fluid. Oligomerization of HCC leads to amyloid deposits in brain arteries at advanced age but this pathological process is greatly accelerated with a naturally occurring Leu68Gln variant, resulting in fatal amyloidosis in early adult life. When proteins are extracted from human cystatin C amyloid deposits, an N-terminally truncated cystatin C (THCC) is found, lacking the first ten amino acid residues of the native sequence. It has been shown that the cerebrospinal fluid may cause this N-terminal truncation, possibly because of disintegration of the leucocytes normally present in this fluid, and the release of leucocyte proteolytic enzymes. HCC is the first disease-causing amyloidogenic protein for which oligomerization via 3D domain swapping has been observed. The aggregates arise in the crystallization buffer and have the form of 2-fold symmetric dimers in which a long alpha-helix of one molecule, flanked by two adjacent beta-strands, has replaced an identical domain of the other molecule, and vice versa. Consistent with a conformational change at one of the beta-hairpin loops of the binding epitope, the dimers (and also any other oligomers, including amyloid aggregates) are inactive as papain inhibitors. Here, we report the structure of N-truncated HCC, the dominant form of cystatin C in amyloid deposits. Although the protein crystallized under conditions that are drastically different from those for the full-length protein, the structure reveals dimerization by the same act of domain swapping. However, the new crystal structure is composed of four independent HCC dimers, none of which has the exact 2-fold symmetry of the full-length dimer. While the four dimers have the same overall topology, the exact relation between the individual domains shows a variability that reflects the flexibility at the dimer-specific open interface, which in the case of 3D domain-swapped HCC consists of beta-interactions between the open hinge loops and results in an unusually long intermolecular beta-sheet. The dimers are engaged in further quaternary interactions resulting in spherical, closed octameric assemblies that are identical to that present in the crystal of the full-length protein. The octamers interact via hydrophobic patches formed on the surface of the domain-swapped dimers as well as by extending the dimer beta-sheet through intermolecular contacts.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Superposition of the CD (blue) and GH (red) THCC dimers on the crystallographic XX0 dimer of full- length HCC (gray), shown in two orientations, (a) and (b), illustrating the flexibility of the open interface. The superpositions were calculated in ALIGN, 27 using the C a atoms from only one half (left-hand-side) of the mol- ecules. The differences in the dimer geometry are there- fore emphasized in the right-hand-side domain. Figure prepared in ViewerLite (http://www.accelrys.com).
Figure 7.
Figure 7. b-Sheet-type interaction between THCC dimers (AB and GH) in two adjacent octamers. This interaction extends the molecular b-sheet of each dimer (built from segments of two molecules in each case) into an intermolecular context. The b-sheets within the dimeric fold are antiparallel; the intermolecular inter- action is parallel. Note the water molecule sealing the gap between the quickly diverging b2 strands. Figure prepared in ViewerLite (http://www.accelrys.com).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 151-160) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19898742 A.Rostagno, J.L.Holton, T.Lashley, T.Revesz, and J.Ghiso (2010).
Cerebral amyloidosis: amyloid subunits, mutants and phenotypes.
  Cell Mol Life Sci, 67, 581-600.  
20976204 C.H.Chu, W.C.Lo, H.W.Wang, Y.C.Hsu, J.K.Hwang, P.C.Lyu, T.W.Pai, and C.Y.Tang (2010).
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.
  PLoS One, 5, e13361.  
20173099 D.Wildes, and J.A.Wells (2010).
Sampling the N-terminal proteome of human blood.
  Proc Natl Acad Sci U S A, 107, 4561-4566.  
20175878 R.Kolodziejczyk, K.Michalska, A.Hernandez-Santoyo, M.Wahlbom, A.Grubb, and M.Jaskolski (2010).
Crystal structure of human cystatin C stabilized against amyloid formation.
  FEBS J, 277, 1726-1737.
PDB code: 3gax
20091872 R.P.Nagarkar, R.A.Hule, D.J.Pochan, and J.P.Schneider (2010).
Domain swapping in materials design.
  Biopolymers, 94, 141-155.  
  19812735 J.H.Zhao, H.L.Liu, H.Y.Lin, C.H.Huang, H.W.Fang, S.S.Chen, Y.Ho, W.B.Tsai, and W.Y.Chen (2008).
Chemical chaperone and inhibitor discovery: potential treatments for protein conformational diseases.
  Perspect Medicin Chem, 1, 39-48.  
17470433 M.Wahlbom, X.Wang, V.Lindström, E.Carlemalm, M.Jaskolski, and A.Grubb (2007).
Fibrillogenic oligomers of human cystatin C are formed by propagated domain swapping.
  J Biol Chem, 282, 18318-18326.  
17439156 Y.M.Lin, H.L.Liu, J.H.Zhao, C.H.Huang, H.W.Fang, Y.Ho, and W.Y.Chen (2007).
Molecular dynamics simulations to investigate the domain swapping mechanism of human cystatin C.
  Biotechnol Prog, 23, 577-584.  
16601115 A.W.Schüttelkopf, G.Hamilton, C.Watts, and D.M.van Aalten (2006).
Structural basis of reduction-dependent activation of human cystatin F.
  J Biol Chem, 281, 16570-16575.
PDB code: 2ch9
16612983 E.Levy, M.Jaskolski, and A.Grubb (2006).
The role of cystatin C in cerebral amyloid angiopathy and stroke: cell biology and animal models.
  Brain Pathol, 16, 60-70.  
16434741 J.He, Y.Song, N.Ueyama, A.Saito, H.Azakami, and A.Kato (2006).
Prevention of amyloid fibril formation of amyloidogenic chicken cystatin by site-specific glycosylation in yeast.
  Protein Sci, 15, 213-222.  
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
16698921 Z.Guo, and D.Eisenberg (2006).
Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I.
  Proc Natl Acad Sci U S A, 103, 8042-8047.  
15596505 A.Merlino, M.A.Ceruso, L.Vitagliano, and L.Mazzarella (2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
  Biophys J, 88, 2003-2012.  
16321154 J.N.Baraniuk, B.Casado, H.Maibach, D.J.Clauw, L.K.Pannell, and S.Hess S (2005).
A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.
  BMC Neurol, 5, 22.  
16170782 R.Janowski, M.Kozak, M.Abrahamson, A.Grubb, and M.Jaskolski (2005).
3D domain-swapped human cystatin C with amyloidlike intermolecular beta-sheets.
  Proteins, 61, 570-578.
PDB code: 1tij
16202603 R.W.Carrell (2005).
Cell toxicity and conformational disease.
  Trends Cell Biol, 15, 574-580.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.