3EHV

X-ray structure of human ubiquitin Zn(II) adduct

• PDB DOI: https://doi.org/10.2210/pdb3EHV/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-15 Released: 2009-03-17 
• Deposition Author(s): Falini, G., Fermani, S., Tosi, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.271 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

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: 5960-5962

• PubMed: 19030552 
• DOI: https://doi.org/10.1039/b813463d
• Primary Citation of Related Structures:  
  3EEC, 3EFU, 3EHV


• PubMed Abstract: 
  

  A structural investigation performed on adducts of human ubiquitin with group-12 metal ions reveals common preferential anchoring sites, the most populated one being His68; at higher metal ion concentration a second and a third site, close to the N-terminus of the protein, become populated and promote a polymorphic transition from orthorhombic to cubic form; Glu16 and Glu18, involved in the latter metal binding, undergo a remarkable displacement from their position in native ubiquitin; the aggregate stereochemistry appears to be driven by the clustering of deshielded backbone hydrogen-bond patches, and metal ions foster this process.

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Organizational Affiliation: 

Dipartimento di Chimica, G. Ciamician, Università di Bologna, via Selmi 2, 40126, Bologna, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.8 kDa 
• Atom Count: 1,831 
• Modelled Residue Count: 214 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, 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 GTEx:  ENSG00000150991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.271 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.357	α = 90
b = 50.946	β = 90
c = 93.317	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Falini, G., Fermani, S., Tosi, G.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-11-13
  Changes: Data collection
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description