6XX0

Crystal structure of NEMO in complex with Ubv-LIN

Summary for 6XX0

• Entry DOI: 10.2210/pdb6xx0/pdb
• Descriptor: Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b, Ubv-LIN (3 entities in total)
• Functional Keywords: inhibitor, ubiquitin, protein binding
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 38561.92

Authors

Akutsu, M.,Skenderovic, A.,Garcia-Pardo, J.,Maculins, T.,Dikic, I. (deposition date: 2020-01-26, release date: 2021-02-03, Last modification date: 2024-01-24)

Primary citation

Maculins, T.,Garcia-Pardo, J.,Skenderovic, A.,Gebel, J.,Putyrski, M.,Vorobyov, A.,Busse, P.,Varga, G.,Kuzikov, M.,Zaliani, A.,Rahighi, S.,Schaeffer, V.,Parnham, M.J.,Sidhu, S.S.,Ernst, A.,Dotsch, V.,Akutsu, M.,Dikic, I.
Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms.
Cell Chem Biol, 27:1441-1451.e7, 2020

PubMed Abstract: Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.

PubMed: 32726587
DOI: 10.1016/j.chembiol.2020.07.010

Experimental method

X-RAY DIFFRACTION (2.6 Å)