7T8J

The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a GSGG linker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain.

Nawarathnage, S.Tseng, Y.J.Soleimani, S.Smith, T.Pedroza Romo, M.J.Abiodun, W.O.Egbert, C.M.Madhusanka, D.Bunn, D.Woods, B.Tsubaki, E.Stewart, C.Brown, S.Doukov, T.Andersen, J.L.Moody, J.D.

(2023) Structure 31: 1589

  • DOI: https://doi.org/10.1016/j.str.2023.09.001
  • Primary Citation of Related Structures:  
    7T8J, 7TCY, 7TDY, 7U4W, 7U4Z

  • PubMed Abstract: 

    Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1 ubiquitin-associated (UBA) domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. No experimentally determined molecular structure of this unusual UBA domain is available. We fused the UBA domain to the 1TEL variant of the translocation ETS leukemia protein sterile alpha motif (TELSAM) crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and crystallize at protein concentrations as low as 0.2 mg/mL. Our studies support a mechanism of 1TEL fusion crystallization and show that 1TEL fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1157Homo sapiensMutation(s): 4 
Gene Names: ETV6TELTEL1TNK1
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P41212 (Homo sapiens)
Explore P41212 
Go to UniProtKB:  P41212
PHAROS:  P41212
GTEx:  ENSG00000139083 
Find proteins for Q13470 (Homo sapiens)
Explore Q13470 
Go to UniProtKB:  Q13470
PHAROS:  Q13470
GTEx:  ENSG00000174292 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41212Q13470
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 65
  • Diffraction Data: https://doi.org/10.18430/M37T8J
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.651α = 90
b = 68.651β = 90
c = 56.735γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
autoPROCdata scaling
PHASERphasing
Cootmodel building
autoPROCdata processing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Refinement description
  • Version 2.0: 2023-03-22
    Changes: Advisory, Atomic model, Database references, Polymer sequence, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 2.2: 2023-11-15
    Changes: Database references
  • Version 2.3: 2023-12-20
    Changes: Database references