7OOJ

Structure of D-Thr53 Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A litmus test for classifying recognition mechanisms of transiently binding proteins.

Chakrabarti, K.S.Olsson, S.Pratihar, S.Giller, K.Overkamp, K.Lee, K.O.Gapsys, V.Ryu, K.S.de Groot, B.L.Noe, F.Becker, S.Lee, D.Weikl, T.R.Griesinger, C.

(2022) Nat Commun 13: 3792-3792

  • DOI: 10.1038/s41467-022-31374-5
  • Primary Citation of Related Structures:  
    7OOJ

  • PubMed Abstract: 
  • Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments ...

    Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin's paradigmatic interaction with an SH3 (Src-homology 3) domain. By contrast, the SH3 domain recognizes ubiquitin in a two-state binding process. Subsequent molecular dynamics simulations and Markov state modeling reveal that the ubiquitin conformation selected for binding exhibits a characteristically extended C-terminus. Our framework is robust and expandable for implementation in other binding scenarios with the potential to show that conformational selection might be the design principle of the hubs in protein interaction networks.


    Organizational Affiliation

    Department of NMR Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. cigr@nmr.mpibpc.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA, B76Homo sapiensMutation(s): 1 
Gene Names: RPS27AUBA80UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens)
Explore P62979 
Go to UniProtKB:  P62979
PHAROS:  P62979
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62979
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.479α = 90
b = 105.479β = 90
c = 105.479γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2021-05-27 
  • Released Date: 2022-05-18 
  • Deposition Author(s): Becker, S.

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references