Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 

Starting Model: experimental
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Crystallographic analysis of metal-ion binding to human ubiquitin.

Arnesano, F.Belviso, B.D.Caliandro, R.Falini, G.Fermani, S.Natile, G.Siliqi, D.

(2011) Chemistry 17: 1569-1578

  • DOI: https://doi.org/10.1002/chem.201001617
  • Primary Citation of Related Structures:  
    3N30, 3N32

  • PubMed Abstract: 

    The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.

  • Organizational Affiliation

    Dipartimento Farmaco-Chimico, University of Bari A. Moro, via E. Orabona 4, 70125 Bari, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.89α = 90
b = 104.89β = 90
c = 104.89γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
ILMILIONEmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description