8VC8

Crystal structure of heme-loaded design: HEM_3.C9

8VC8 の概要

• エントリーDOI: 10.2210/pdb8vc8/pdb
• 分子名称: HEM_3.C9, SULFATE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (4 entities in total)
• 機能のキーワード: de novo design, rfdiffusion, alphafold2, rosettafold, de novo protein
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 22852.18

構造登録者

Kalvet, I.,Bera, A.K.,Baker, D. (登録日: 2023-12-13, 公開日: 2024-03-20, 最終更新日: 2024-05-01)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.8 Å)