7UPM

Tribbles (TRIB2) pseudokinase bound to nanobody Nb4.103


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Nanobodies identify an activated state of the TRIB2 pseudokinase.

Jamieson, S.A.Pudjihartono, M.Horne, C.R.Viloria, J.S.Dunlop, J.L.McMillan, H.D.Day, R.C.Keeshan, K.Murphy, J.M.Mace, P.D.

(2022) Structure 30: 1518

  • DOI: https://doi.org/10.1016/j.str.2022.08.006
  • Primary Citation of Related Structures:  
    7UPM

  • PubMed Abstract: 

    Tribbles proteins (TRIB1-3) are pseudokinases that recruit substrates to the COP1 ubiquitin ligase. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukemia oncogene, because it recruits the C/EBPα transcription factor for ubiquitination by COP1. Here we report identification of nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of the TRIB2-Nb4.103 complex identified the nanobody to bind the N-terminal lobe of TRIB2, enabling specific recognition of TRIB2 in an activated conformation that is similar to the C/EBPα-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilize a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors and nanobody tools for future investigation of TRIB2 function.


  • Organizational Affiliation

    Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tribbles homolog 2264Homo sapiensMutation(s): 0 
Gene Names: TRIB2TRB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92519 (Homo sapiens)
Explore Q92519 
Go to UniProtKB:  Q92519
PHAROS:  Q92519
GTEx:  ENSG00000071575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92519
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nb4.103 Nanobody122synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.207 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.16α = 90
b = 75.16β = 90
c = 273.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden FundNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-10-12
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description