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PDBsum entry 1g96

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protein ligands metals links
Hydrolase inhibitor PDB id
1g96
Jmol
Contents
Protein chain
111 a.a. *
Ligands
GOL
Metals
_CL
Waters ×22
* Residue conservation analysis
PDB id:
1g96
Name: Hydrolase inhibitor
Title: Human cystatin c; dimeric form with 3d domain swapping
Structure: Cystatin c. Chain: a. Synonym: gamma-trace, post-gamma-globulin. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
2.50Å     R-factor:   0.220     R-free:   0.249
Authors: R.Janowski,M.Kozak,E.Jankowska,Z.Grzonka,A.Grubb,M.Abrahamso M.Jaskolski
Key ref:
R.Janowski et al. (2001). Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping. Nat Struct Biol, 8, 316-320. PubMed id: 11276250 DOI: 10.1038/86188
Date:
22-Nov-00     Release date:   06-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   14 terms 
  Biological process     cell activation   35 terms 
  Biochemical function     protein binding     6 terms  

 

 
DOI no: 10.1038/86188 Nat Struct Biol 8:316-320 (2001)
PubMed id: 11276250  
 
 
Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping.
R.Janowski, M.Kozak, E.Jankowska, Z.Grzonka, A.Grubb, M.Abrahamson, M.Jaskolski.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Primary, secondary, tertiary and quaternary structure of HCC. a, Amino acid sequence of HCC with assignment of secondary structure elements derived from the crystal structure. Blue, N-terminal fragment not visible in electron density; green, linker strand corresponding to loop L1 in monomeric chicken cystatin; magenta, loop L2; red, site of the L68Q mutation. b, The fold of chicken cystatin (PDB entry 1CEW), defining the topology of this class of proteins. c, Domain-swapped dimer of HCC in a view similar to (b) (top) and in a perpendicular orientation (bottom) emphasizing the -sheet in the domain switch region ('open interface') and the site of the L68Q mutation (red dot).
Figure 2.
Figure 2. Schematic illustrations of how HCC oligomers are formed. a, Two monomers form a dimer through b, three-dimensional domain swapping. c, In an open-ended variant, the same mechanism may lead to cross -fibril structure. In this diagram, the cystatin fold is represented by an -helix (cylinder) running across the concave face of a -sheet (stripes). In a screw operation, new components are added by rotation followed by a translation along the screw axis.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 316-320) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131979 C.Liu, M.R.Sawaya, and D.Eisenberg (2011).
β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.
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PDB codes: 3low 3loz
21220305 K.Domanska, S.Vanderhaegen, V.Srinivasan, E.Pardon, F.Dupeux, J.A.Marquez, S.Giorgetti, M.Stoppini, L.Wyns, V.Bellotti, and J.Steyaert (2011).
Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic {beta}2-microglobulin variant.
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PDB code: 2x89
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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).
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The crystal structures of two salivary cystatins from the tick Ixodes scapularis and the effect of these inhibitors on the establishment of Borrelia burgdorferi infection in a murine model.
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PDB codes: 3lh4 3li7 3mwz
20920298 N.F.Valadares, M.Dellamano, A.Soares-Costa, F.Henrique-Silva, and R.C.Garratt (2010).
Molecular determinants of improved cathepsin B inhibition by new cystatins obtained by DNA shuffling.
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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.
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PDB code: 3gax
20091872 R.P.Nagarkar, R.A.Hule, D.J.Pochan, and J.P.Schneider (2010).
Domain swapping in materials design.
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19247429 B.Raveh, A.Enosh, O.Schueler-Furman, and D.Halperin (2009).
Rapid sampling of molecular motions with prior information constraints.
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19129192 K.Herz, A.Rimon, G.Jeschke, and E.Padan (2009).
{beta}-Sheet-dependent Dimerization Is Essential for the Stability of NhaA Na+/H+ Antiporter.
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18636508 K.Skerget, A.Vilfan, M.Pompe-Novak, V.Turk, J.P.Waltho, D.Turk, and E.Zerovnik (2009).
The mechanism of amyloid-fibril formation by stefin B: temperature and protein concentration dependence of the rates.
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19074157 L.A.Clark, P.A.Boriack-Sjodin, E.Day, J.Eldredge, C.Fitch, M.Jarpe, S.Miller, Y.Li, K.Simon, and H.W.van Vlijmen (2009).
An antibody loop replacement design feasibility study and a loop-swapped dimer structure.
  Protein Eng Des Sel, 22, 93.
PDB code: 3eot
19137579 S.Rodziewicz-Motowidło, J.Iwaszkiewicz, R.Sosnowska, P.Czaplewska, E.Sobolewski, A.Szymańska, K.Stachowiak, and A.Liwo (2009).
The role of the Val57 amino-acid residue in the hinge loop of the human cystatin C. Conformational studies of the beta2-L1-beta3 segments of wild-type human cystatin C and its mutants.
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18620534 A.Shukla, M.Raje, and P.Guptasarma (2008).
Coalescence of spherical beads of retro-HSP12.6 into linear and ring-shaped amyloid nanofibers.
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18783611 C.Serbielle, S.Chowdhury, S.Pichon, S.Dupas, J.Lesobre, E.O.Purisima, J.M.Drezen, and E.Huguet (2008).
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18925453 S.Ceru, S.J.Kokalj, S.Rabzelj, M.Skarabot, I.Gutierrez-Aguirre, N.Kopitar-Jerala, G.Anderluh, D.Turk, V.Turk, and E.Zerovnik (2008).
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18632274 S.Zhu (2008).
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17701471 E.Zerovnik, M.Skarabot, K.Skerget, S.Giannini, V.Stoka, S.Jenko-Kokalj, and R.A.Staniforth (2007).
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Focus on molecules: cystatin C.
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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.
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17391511 V.Alva, M.Ammelburg, J.Söding, and A.N.Lupas (2007).
On the origin of the histone fold.
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Molecular dynamics simulations to investigate the domain swapping mechanism of human cystatin C.
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16612982 A.Palsdottir, A.O.Snorradottir, and L.Thorsteinsson (2006).
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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
16981672 D.Eisenberg, R.Nelson, M.R.Sawaya, M.Balbirnie, S.Sambashivan, M.I.Ivanova, A...Madsen, and C.Riekel (2006).
The structural biology of protein aggregation diseases: Fundamental questions and some answers.
  Acc Chem Res, 39, 568-575.  
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.  
16939620 E.Zerovnik, K.Skerget, M.Tusek-Znidaric, C.Loeschner, M.W.Brazier, and D.R.Brown (2006).
High affinity copper binding by stefin B (cystatin B) and its role in the inhibition of amyloid fibrillation.
  FEBS J, 273, 4250-4263.  
16407060 F.Ding, K.C.Prutzman, S.L.Campbell, and N.V.Dokholyan (2006).
Topological determinants of protein domain swapping.
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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.
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16342276 M.Kenig, S.Jenko-Kokalj, M.Tusek-Znidaric, M.Pompe-Novak, G.Guncar, D.Turk, J.P.Waltho, R.A.Staniforth, F.Avbelj, and E.Zerovnik (2006).
Folding and amyloid-fibril formation for a series of human stefins' chimeras: any correlation?
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16963458 M.R.Ho, Y.C.Lou, W.C.Lin, P.C.Lyu, W.N.Huang, and C.Chen (2006).
Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation.
  J Biol Chem, 281, 33566-33576.
PDB code: 2go0
16519682 M.Rodríguez, A.Benito, M.Ribó, and M.Vilanova (2006).
Characterization of the dimerization process of a domain-swapped dimeric variant of human pancreatic ribonuclease.
  FEBS J, 273, 1166-1176.  
16563741 R.Nelson, and D.Eisenberg (2006).
Recent atomic models of amyloid fibril structure.
  Curr Opin Struct Biol, 16, 260-265.  
16831167 T.Jiborn, M.Abrahamson, V.Gadaleanu, A.Lundwall, and A.Bjartell (2006).
Aberrant expression of cystatin C in prostate cancer is associated with neuroendocrine differentiation.
  BJU Int, 98, 189-196.  
17014390 V.S.Vaidya, and J.V.Bonventre (2006).
Mechanistic biomarkers for cytotoxic acute kidney injury.
  Expert Opin Drug Metab Toxicol, 2, 697-713.  
16415060 Y.B.Yan, J.Zhang, H.W.He, and H.M.Zhou (2006).
Oligomerization and aggregation of bovine pancreatic ribonuclease A: characteristic events observed by FTIR spectroscopy.
  Biophys J, 90, 2525-2533.  
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.  
15689507 L.A.Clark (2005).
Protein aggregation determinants from a simplified model: cooperative folders resist aggregation.
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15728581 M.Alvarez-Fernandez, Y.H.Liang, M.Abrahamson, and X.D.Su (2005).
Crystal structure of human cystatin D, a cysteine peptidase inhibitor with restricted inhibition profile.
  J Biol Chem, 280, 18221-18228.
PDB codes: 1rn7 1roa
15906014 M.Brage, M.Abrahamson, V.Lindström, A.Grubb, and U.H.Lerner (2005).
Different cysteine proteinases involved in bone resorption and osteoclast formation.
  Calcif Tissue Int, 76, 439-447.  
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
16152647 S.D.Khare, K.C.Wilcox, P.Gong, and N.V.Dokholyan (2005).
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation.
  Proteins, 61, 617-632.  
16155205 S.Rabzelj, V.Turk, and E.Zerovnik (2005).
In vitro study of stability and amyloid-fibril formation of two mutants of human stefin B (cystatin B) occurring in patients with EPM1.
  Protein Sci, 14, 2713-2722.  
16204848 S.S.Cho, Y.Levy, J.N.Onuchic, and P.G.Wolynes (2005).
Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation.
  Phys Biol, 2, S44-S55.  
16081531 T.Cellmer, D.Bratko, J.M.Prausnitz, and H.Blanch (2005).
Protein-folding landscapes in multichain systems.
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15752368 T.Langerholc, V.Zavasnik-Bergant, B.Turk, V.Turk, M.Abrahamson, and J.Kos (2005).
Inhibitory properties of cystatin F and its localization in U937 promonocyte cells.
  FEBS J, 272, 1535-1545.  
15531601 X.Yuan, and C.Bystroff (2005).
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.
  Bioinformatics, 21, 1010-1019.  
15218036 G.Gotte, and M.Libonati (2004).
Oligomerization of ribonuclease A: two novel three-dimensional domain-swapped tetramers.
  J Biol Chem, 279, 36670-36679.  
15249659 M.I.Ivanova, M.R.Sawaya, M.Gingery, A.Attinger, and D.Eisenberg (2004).
An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril.
  Proc Natl Acad Sci U S A, 101, 10584-10589.  
14691222 M.Kenig, S.Berbić, A.Krijestorac, L.Kroon-Zitko, M.Tusek, M.Pompe-Novak, and E.Zerovnik (2004).
Differences in aggregation properties of three site-specific mutants of recombinant human stefin B.
  Protein Sci, 13, 63-70.  
15028721 M.Nilsson, X.Wang, S.Rodziewicz-Motowidlo, R.Janowski, V.Lindström, P.Onnerfjord, G.Westermark, Z.Grzonka, M.Jaskolski, and A.Grubb (2004).
Prevention of domain swapping inhibits dimerization and amyloid fibril formation of cystatin C: use of engineered disulfide bridges, antibodies, and carboxymethylpapain to stabilize the monomeric form of cystatin C.
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Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin.
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Domain swapping of CD4 upon dimerization.
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Glycosylation and specific deamidation of ribonuclease B affect the formation of three-dimensional domain-swapped oligomers.
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14627730 T.Scheuermann, B.Schulz, A.Blume, E.Wahle, R.Rudolph, and E.Schwarz (2003).
Trinucleotide expansions leading to an extended poly-L-alanine segment in the poly (A) binding protein PABPN1 cause fibril formation.
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The dual role of a loop with low loop contact distance in folding and domain swapping.
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12360234 D.A.Lomas, and R.W.Carrell (2002).
Serpinopathies and the conformational dementias.
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Familial conformational diseases and dementias.
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Crystal structure of the FHA domain of the Chfr mitotic checkpoint protein and its complex with tungstate.
  Structure, 10, 891-899.
PDB codes: 1lgp 1lgq
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Amyloid-fibril formation. Proposed mechanisms and relevance to conformational disease.
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12108553 E.Zerovnik, V.Zavasnik-Bergant, N.Kopitar-Jerala, M.Pompe-Novak, M.Skarabot, K.Goldie, M.Ravnikar, I.Musevic, and V.Turk (2002).
Amyloid fibril formation by human stefin B in vitro: immunogold labelling and comparison to stefin A.
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Overexpression and structural study of the cathelicidin motif of the protegrin-3 precursor.
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12065604 J.Hong, K.Yoshida, and M.R.Rosner (2002).
Characterization of a cysteine proteinase inhibitor induced during neuronal cell differentiation.
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Integrin structure: new twists and turns in dynamic cell adhesion.
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Protein folding and three-dimensional domain swapping: a strained relationship?
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The role of dimerization in prion replication.
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Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics.
  Protein Sci, 11, 1036-1049.  
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3D domain swapping: as domains continue to swap.
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Crystal structure of the extracellular segment of integrin alpha Vbeta3.
  Science, 294, 339-345.
PDB code: 1jv2
11532941 R.A.Staniforth, S.Giannini, L.D.Higgins, M.J.Conroy, A.M.Hounslow, R.Jerala, C.J.Craven, and J.P.Waltho (2001).
Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily.
  EMBO J, 20, 4774-4781.
PDB code: 1n9j
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