5TOG

Room temperature structure of ubiquitin variant u7ub25.2540

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • 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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.str.2017.03.009
  • Primary Citation of Related Structures:  

  • 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 ...

    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 Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
A
78Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.103 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 43.920α = 90.00
b = 43.920β = 90.00
c = 55.440γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Refinement description
  • Version 1.2: 2019-11-27
    Type: Author supporting evidence