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Title | AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography. |
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Journal, issue, pages | Acta Crystallogr D Struct Biol, Vol. 80, Issue Pt 4, Page 270-278, Year 2024 |
Publish date | Apr 1, 2024 |
![]() | Justin E Miller / Matthew P Agdanowski / Joshua L Dolinsky / Michael R Sawaya / Duilio Cascio / Jose A Rodriguez / Todd O Yeates / ![]() |
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 ...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. |
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Methods | X-ray diffraction / EM (electron crystallography) |
Resolution | 2.1 - 3 Å |
Structure data | ![]() PDB-8t0b: ![]() PDB-8t1m: ![]() PDB-8t1n: |
Chemicals | ![]() ChemComp-HOH: |
Source |
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![]() | UNKNOWN FUNCTION / AlphaFold / Bacterial Protein / Domain of Unknown Function / Novel Fold / Micro-ED |