3EFU | pdb_00003efu

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

• PDB DOI: https://doi.org/10.2210/pdb3EFU/pdb

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


• Deposited: 2008-09-10 Released: 2008-12-09 
• Deposition Author(s): Falini, G., Fermani, S., Tosi, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.293 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

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 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)

Macromolecule Content 

• Total Structure Weight: 8.78 kDa 
• Atom Count: 693 
• Modeled Residue Count: 72 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
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
HG	B [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.293 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.024	α = 90
b = 42.828	β = 90
c = 50.374	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Falini, G., Fermani, S., Tosi, G.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description