2K39

Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 116 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6V5D


Literature

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.

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

(2008) Science 320: 1471-1475

  • DOI: https://doi.org/10.1126/science.1157092
  • Primary Citation of Related Structures:  
    2K39

  • PubMed Abstract: 

    Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.


  • Organizational Affiliation

    Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin76Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62972 (Xenopus laevis)
Explore P62972 
Go to UniProtKB:  P62972
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UniProt GroupP62972
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 116 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-11-13
    Changes: Data collection, Derived calculations, Experimental preparation, Source and taxonomy, Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references