7UPQ

Crystal structure of designed heterotrimeric assembly DHT03_1arm_A21/B/C

Summary for 7UPQ

• Entry DOI: 10.2210/pdb7upq/pdb
• Descriptor: DHT03 protein A, DHT03 protein B, DHT03 protein C (3 entities in total)
• Functional Keywords: de novo designed protein, de novo protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 12
• Total formula weight: 162701.20

Authors

Chang, Y.,Bhabha, G.,Ekiert, D.C. (deposition date: 2022-04-16, release date: 2022-12-14, Last modification date: 2024-04-03)

Primary citation

Bermeo, S.,Favor, A.,Chang, Y.T.,Norris, A.,Boyken, S.E.,Hsia, Y.,Haddox, H.K.,Xu, C.,Brunette, T.J.,Wysocki, V.H.,Bhabha, G.,Ekiert, D.C.,Baker, D.
De novo design of obligate ABC-type heterotrimeric proteins.
Nat.Struct.Mol.Biol., 29:1266-1276, 2022

PubMed Abstract: The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.

PubMed: 36522429
DOI: 10.1038/s41594-022-00879-4

Experimental method

X-RAY DIFFRACTION (3.35 Å)