8T1N

Micro-ED Structure of a Novel Domain of Unknown Function Solved with AlphaFold

Summary for 8T1N

• Entry DOI: 10.2210/pdb8t1n/pdb
• Related: 8T0B 8T1M
• Descriptor: DUF1842 domain-containing protein (1 entity in total)
• Functional Keywords: alphafold, bacterial protein, domain of unknown function, novel fold, unknown function, micro-ed
• Biological source: Burkholderia pseudomallei
• Total number of polymer chains: 2
• Total formula weight: 46628.51

Authors

Miller, J.E.,Cascio, D.,Sawaya, M.R.,Cannon, K.A.,Rodriguez, J.A.,Yeates, T.O. (deposition date: 2023-06-02, release date: 2024-01-17, Last modification date: 2024-04-10)

Primary citation

Miller, J.E.,Agdanowski, M.P.,Dolinsky, J.L.,Sawaya, M.R.,Cascio, D.,Rodriguez, J.A.,Yeates, T.O.
AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography.
Acta Crystallogr D Struct Biol, 80:270-278, 2024

PubMed Abstract: Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

PubMed: 38451205
DOI: 10.1107/S205979832400072X

Experimental method

ELECTRON CRYSTALLOGRAPHY (3 Å)