Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14032.24 
• Atom Count: 915 
• Residue Count: 120 
• 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): 1 


• 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 

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.,Sect.D 69: 577-586

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


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cystatin-C	A	120	Homo sapiens	Mutation(s): 1  Gene Names: CST3
Find proteins for P01034 (Homo sapiens) Go to Gene View: CST3 Go to UniProtKB:  P01034

Small Molecules

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

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 140.135	α = 90.00
b = 140.135	β = 90.00
c = 140.135	γ = 90.00

Software Package:

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

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
  Type: Derived calculations
• Version 1.2: 2013-04-03
  Type: Database references