8VC8

Crystal structure of heme-loaded design: HEM_3.C9

Summary for 8VC8

• Entry DOI: 10.2210/pdb8vc8/pdb
• Descriptor: HEM_3.C9, SULFATE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (4 entities in total)
• Functional Keywords: de novo design, rfdiffusion, alphafold2, rosettafold, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 22852.18

Authors

Kalvet, I.,Bera, A.K.,Baker, D. (deposition date: 2023-12-13, release date: 2024-03-20, Last modification date: 2024-05-01)

Primary citation

Krishna, R.,Wang, J.,Ahern, W.,Sturmfels, P.,Venkatesh, P.,Kalvet, I.,Lee, G.R.,Morey-Burrows, F.S.,Anishchenko, I.,Humphreys, I.R.,McHugh, R.,Vafeados, D.,Li, X.,Sutherland, G.A.,Hitchcock, A.,Hunter, C.N.,Kang, A.,Brackenbrough, E.,Bera, A.K.,Baek, M.,DiMaio, F.,Baker, D.
Generalized biomolecular modeling and design with RoseTTAFold All-Atom.
Science, 384:eadl2528-eadl2528, 2024

PubMed Abstract: Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.

PubMed: 38452047
DOI: 10.1126/science.adl2528

Experimental method

X-RAY DIFFRACTION (1.8 Å)