5TOG

Room temperature structure of ubiquitin variant u7ub25.2540

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-10-17 Released: 2017-05-24 
  • Deposition Author(s): Biel, J.T., Thompson, M.C., Cunningham, C.N., Corn, J.E., Fraser, J.S.
  • Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.

Biel, J.T.Thompson, M.C.Cunningham, C.N.Corn, J.E.Fraser, J.S.

(2017) Structure 25: 739-749.e3

  • DOI: https://doi.org/10.1016/j.str.2017.03.009
  • Primary Citation of Related Structures:  
    5TOF, 5TOG

  • PubMed Abstract: 

    Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional conformations. To test this idea, we exploited advances in multiconformer modeling of room-temperature X-ray data collection on redesigned ubiquitin variants selected for increasing binding affinity to the deubiquitinase USP7. Initial core mutations disrupt natural packing and lead to increased flexibility. Additional, experimentally selected mutations quenched conformational heterogeneity through new stabilizing interactions. Stabilizing interactions, such as cation-pi stacking and ordered waters, which are not included in standard protein design energy functions, can create specific interactions that have long-range effects on flexibility across the protein. Our results suggest that increasing flexibility may be a useful strategy to escape local minima during initial directed evolution and protein design steps when creating new functions.


  • Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B78Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.92α = 90
b = 43.92β = 90
c = 55.44γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesDP5 OD009180
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR21 GM110580
National Science Foundation (NSF, United States)United StatesSTC-1231306
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF32 HL129989

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Refinement description
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description