5NL4

Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium.

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

(2018) Chemistry 24: 4140-4148

  • DOI: 10.1002/chem.201705543
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitin-positive protein aggregates are biomarkers of neurodegeneration, but the molecular mechanism responsible for their formation and accumulation is still unclear. Possible aggregation pathways of human ubiquitin (hUb) promoted by both intrinsi ...

    Ubiquitin-positive protein aggregates are biomarkers of neurodegeneration, but the molecular mechanism responsible for their formation and accumulation is still unclear. Possible aggregation pathways of human ubiquitin (hUb) promoted by both intrinsic and extrinsic factors, are here investigated. By a computational analysis, two different hUb dimers are indicated as possible precursors of amyloid-like structures, but their formation is disfavored by an electrostatic repulsion involving Glu16 and other carboxylate residues present at the dimer interface. Experimental data on the E16V mutant of hUb shows that this single-point mutation, although not affecting the overall protein conformation, promotes protein aggregation. It is sufficient to shift the same mutation by only two residues (E18V) to regain the behavior of wild-type hUb. The neutralization of Glu16 negative charge by a metal ion and a decrease of the dielectric constant of the medium by addition of trifluoroethanol (TFE), also promote hUb aggregation. The outcomes of this research have important implications for the prediction of physiological parameters that favor aggregate formation.


    Related Citations: 
    • 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


    Organizational Affiliation

    Universita degli Studi di Bologna, Chemistry "G. Ciamician", via Selmi 2, 40126, Bologna, ITALY.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
A, B, C
76Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.170α = 90.00
b = 50.330β = 90.00
c = 93.850γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
iMOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Database references