6K4I

The partially disordered conformation of ubiquitin (Q41N variant)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1900 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Paramagnetic relaxation enhancement-assisted structural characterization of a partially disordered conformation of ubiquitin.

Wakamoto, T.Ikeya, T.Kitazawa, S.Baxter, N.J.Williamson, M.P.Kitahara, R.

(2019) Protein Sci. 28: 1993-2003

  • DOI: 10.1002/pro.3734

  • PubMed Abstract: 
  • Nuclear magnetic resonance (NMR) is a powerful tool to study three-dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that u ...

    Nuclear magnetic resonance (NMR) is a powerful tool to study three-dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that ubiquitin has two folded conformations, N 1 and N 2 and plus another folded conformation, I, in which some amide group signals of residues 33-41 almost disappeared above 3 kbar at pH 4.5 and 273 K. Thus, well-converged structural models could not be obtained for this region owing to the absence of distance restraints. Here, we reexamine the problem using the ubiquitin Q41N variant as a model for this locally disordered conformation, I. We demonstrate that the variant shows pressure-induced loss of backbone amide group signals at residues 28, 33, 36, and 39-41 like the wild-type, with a similar but smaller effect on CαH and CβH signals. In order to characterize this I structure, we measured paramagnetic relaxation enhancement (PRE) under high pressure to obtain distance restraints, and calculated the structure assisted by Bayesian inference. We conclude that the more disordered I conformation observed at pH 4.0, 278 K, and 2.5 kbar largely retained the N 2 conformation, although the amide groups at residues 33-41 have more heterogeneous conformations and more contact with water, which differ from the N 1 and N 2 states. The PRE-assisted strategy has the potential to improve structural characterization of proteins that lack NMR signals, especially for relatively more open and hydrated protein conformations.


    Organizational Affiliation

    Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.,Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
A
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for J3QS39 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  J3QS39
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1900 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentJapan--

Revision History 

  • Version 1.0: 2019-10-30
    Type: Initial release