6V5D

EROS3 RDC and NOE Derived Ubiquitin Ensemble


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 800 
  • Conformers Submitted: 176 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2K39 - determined by Lange, O.F., Lakomek, N.A., Fares, C., Schroder, G., Walter, K., Becker, S., Meiler, J., Grubmuller, H., Griesinger, C., de Groot, B.L.  

Literature

Enhancing NMR derived ensembles with kinetics on multiple timescales.

Smith, C.A.Mazur, A.Rout, A.K.Becker, S.Lee, D.de Groot, B.L.Griesinger, C.

(2019) J.Biomol.Nmr --: --

  • DOI: 10.1007/s10858-019-00288-8

  • PubMed Abstract: 
  • Nuclear magnetic resonance (NMR) has the unique advantage of elucidating the structure and dynamics of biomolecules in solution at physiological temperatures, where they are in constant movement on timescales from picoseconds to milliseconds. Such mo ...

    Nuclear magnetic resonance (NMR) has the unique advantage of elucidating the structure and dynamics of biomolecules in solution at physiological temperatures, where they are in constant movement on timescales from picoseconds to milliseconds. Such motions have been shown to be critical for enzyme catalysis, allosteric regulation, and molecular recognition. With NMR being particularly sensitive to these timescales, detailed information about the kinetics can be acquired. However, nearly all methods of NMR-based biomolecular structure determination neglect kinetics, which introduces a large approximation to the underlying physics, limiting both structural resolution and the ability to accurately determine molecular flexibility. Here we present the Kinetic Ensemble approach that uses a hierarchy of interconversion rates between a set of ensemble members to rigorously calculate Nuclear Overhauser Effect (NOE) intensities. It can be used to simultaneously refine both temporal and structural coordinates. By generalizing ideas from the extended model free approach, the method can analyze the amplitudes and kinetics of motions anywhere along the backbone or side chains. Furthermore, analysis of a large set of crystal structures suggests that NOE data contains a surprising amount of high-resolution information that is better modeled using our approach. The Kinetic Ensemble approach provides the means to unify numerous types of experiments under a single quantitative framework and more fully characterize and exploit kinetically distinct protein states. While we apply the approach here to the protein ubiquitin and cross validate it with previously derived datasets, the approach can be applied to any protein for which NOE data is available.


    Related Citations: 
    • Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.
      Lange, O.F.,Lakomek, N.A.,Fares, C.,Schroeder, G.F.,Walter, K.F.,Becker, S.,Meiler, J.,Grubmueller, H.,Griesinger, C.,de Groot, B.L.
      (2008) Science 320: 1471


    Organizational Affiliation

    Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. donghan.lee@louisville.edu.,Department of Chemistry, Wesleyan University, Middletown, USA. colin.smith@wesleyan.edu.,Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. bgroot@gwdg.de.,Biozentrum, University of Basel, Basel, Switzerland.,Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. colin.smith@wesleyan.edu.,James Graham Brown Cancer Center, University of Louisville, Louisville, USA. donghan.lee@louisville.edu.,Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. colin.smith@wesleyan.edu.,Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. cigr@nmr.mpibpc.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 800 
  • Conformers Submitted: 176 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release