Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.03 kDa 
• Atom Count: 982 
• Residue Count: 111 
• Unique protein chains: 1

3S67

Crystal structure of V57P mutant of human cystatin C

• DOI: 10.2210/pdb3S67/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-25 Released: 2012-05-30 
• Deposition Author(s): Orlikowska, M., Szymanska, A., Borek, D., Otwinowski, Z., Skowron, P., Jankowska, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.229 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein.

Orlikowska, M., Szymanska, A., Borek, D., Otwinowski, Z., Skowron, P., Jankowska, E.

(2013) Acta Crystallogr D Biol Crystallogr 69: 577-586

• PubMed: 23519666 
• DOI: 10.1107/S0907444912051657
• Primary Citation of Related Structures:  
  3SVA, 3S67


• PubMed Abstract: 
  

Wild-type human cystatin C (hCC wt) is a low-molecular-mass protein (120 amino-acid residues, 13,343 Da) that is found in all nucleated cells. Physiologically, it functions as a potent regulator of cysteine protease activity. While the biologically active hCC wt is a monomeric protein, all crystallization efforts to date have resulted in a three-dimensional domain-swapped dimeric structure. In the recently published structure of a mutated hCC, the monomeric fold was preserved by a stabilization of the conformationally constrained loop L1 caused by a single amino-acid substitution: Val57Asn. Additional hCC mutants were obtained in order to elucidate the relationship between the stability of the L1 loop and the propensity of human cystatin C to dimerize. In one mutant Val57 was substituted by an aspartic acid residue, which is favoured in β-turns, and in the second mutant proline, a residue known for broadening turns, was substituted for the same Val57. Here, 2.26 and 3.0 Å resolution crystal structures of the V57D andV57P mutants of hCC are reported and their dimeric architecture is discussed in terms of the stabilization and destabilization effects of the introduced mutations.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystatin-C	A	120	Homo sapiens	Mutation(s): 1  Gene Names: CST3
Find proteins for P01034 (Homo sapiens) Explore P01034  Go to UniProtKB:  P01034
NIH Common Fund Data Resources
PHAROS  P01034 GTEx  ENSG00000101439

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD	A	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.229 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.135	α = 90
b = 140.135	β = 90
c = 140.135	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-25 
• Released Date: 2012-05-30 
Deposition Author(s): Orlikowska, M., Szymanska, A., Borek, D., Otwinowski, Z., Skowron, P., Jankowska, E.

Revision History 

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Derived calculations
• Version 1.2: 2013-04-03
  Changes: Database references