7TCY | pdb_00007tcy

The ubiquitin-associated domain of human thirty-eight negative kinase I

• PDB DOI: https://doi.org/10.2210/pdb7TCY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-12-29 Released: 2023-01-11 
• Deposition Author(s): Nawarathnage, S., Bunn, R.D., Stewart, C., Doukov, T., Moody, J.D.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

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: 1589-1603.e6

• PubMed: 37776857 
• DOI: https://doi.org/10.1016/j.str.2023.09.001
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA.
Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA.
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA. Electronic address: [e-mail].
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.88 kDa 
• Atom Count: 1,382 
• Modeled Residue Count: 154 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TNK1	A, B	78	Homo sapiens	Mutation(s): 3  Gene Names: TNK1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13470 (Homo sapiens) Explore Q13470  Go to UniProtKB:  Q13470
PHAROS:  Q13470 GTEx:  ENSG00000174292

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FMT	C [auth A], F [auth A], I [auth A], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37TCY

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.734	α = 90
b = 88.07	β = 90
c = 26.497	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Nawarathnage, S., Bunn, R.D., Stewart, C., Doukov, T., Moody, J.D.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2023-12-20
  Changes: Database references