4K7W

Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational selection of ubiquitin quaternary structures driven by zinc ions.

Fermani, S.Falini, G.Calvaresi, M.Bottoni, A.Calo, V.Mangini, V.Arnesano, F.Natile, G.

(2013) Chemistry 19: 15480-15484

  • DOI: 10.1002/chem.201302229
  • Primary Citation of Related Structures:  
    4K7S, 4K7U, 4K7W

  • PubMed Abstract: 
  • Zinc ions bridging two ubiquitin molecules (with His68 at the interface) contribute to select a subset of conformers from the noncovalent dimer ensemble, thus restricting quaternary structure dynamics, which hampers apo-protein crystallization. The type of selected conformer is shown to determine the crystal packing, which varies from orthorhombic to cubic symmetry ...

    Zinc ions bridging two ubiquitin molecules (with His68 at the interface) contribute to select a subset of conformers from the noncovalent dimer ensemble, thus restricting quaternary structure dynamics, which hampers apo-protein crystallization. The type of selected conformer is shown to determine the crystal packing, which varies from orthorhombic to cubic symmetry.


    Related Citations: 
    • 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
    • Structural probing of Zn(II), Cd(II) and Hg(II) binding to human ubiquitin.
      Falini, G., Fermani, S., Tosi, G., Arnesano, F., Natile, G.
      (2008) Chem Commun (Camb) 45: 5960

    Organizational Affiliation

    Department of Chemistry "G. Ciamician", University of Bologna via F. Selmi 2, 40126 Bologna (Italy).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitinA, B, C76Homo sapiensMutation(s): 0 
Gene Names: UBC
EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , J [auth B] , K [auth B] , L [auth C] , M [auth C] , 
D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A], O [auth C], P [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.88α = 90
b = 50.51β = 90
c = 93.95γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references