8CYK

Crystal structure of hallucinated protein HALC1_878

Summary for 8CYK

• Entry DOI: 10.2210/pdb8cyk/pdb
• Descriptor: HALC1_878 (2 entities in total)
• Functional Keywords: de novo design, hallucination protein mpnn, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 31292.31

Authors

Ragotte, R.J.,Bera, A.K.,Milles, L.F.,Wicky, B.I.M.,Baker, D. (deposition date: 2022-05-23, release date: 2022-09-28, Last modification date: 2024-04-03)

Primary citation

Dauparas, J.,Anishchenko, I.,Bennett, N.,Bai, H.,Ragotte, R.J.,Milles, L.F.,Wicky, B.I.M.,Courbet, A.,de Haas, R.J.,Bethel, N.,Leung, P.J.Y.,Huddy, T.F.,Pellock, S.,Tischer, D.,Chan, F.,Koepnick, B.,Nguyen, H.,Kang, A.,Sankaran, B.,Bera, A.K.,King, N.P.,Baker, D.
Robust deep learning-based protein sequence design using ProteinMPNN.
Science, 378:49-56, 2022

PubMed Abstract: Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning-based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo-electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.

PubMed: 36108050
DOI: 10.1126/science.add2187

Experimental method

X-RAY DIFFRACTION (1.65 Å)