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TitleAlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography.
Journal, issue, pagesActa Crystallogr D Struct Biol, Vol. 80, Issue Pt 4, Page 270-278, Year 2024
Publish dateApr 1, 2024
AuthorsJustin E Miller / Matthew P Agdanowski / Joshua L Dolinsky / Michael R Sawaya / Duilio Cascio / Jose A Rodriguez / Todd O Yeates /
PubMed AbstractMacromolecular 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.
External linksActa Crystallogr D Struct Biol / PubMed:38451205 / PubMed Central
MethodsX-ray diffraction / EM (electron crystallography)
Resolution2.1 - 3 Å
Structure data

PDB-8t0b:
Novel Domain of Unknown Function Solved with AlphaFold
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-8t1m:
Novel Domain of Unknown Function Solved with AlphaFold
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-8t1n:
Micro-ED Structure of a Novel Domain of Unknown Function Solved with AlphaFold
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 3.0 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • burkholderia pseudomallei (bacteria)
KeywordsUNKNOWN FUNCTION / AlphaFold / Bacterial Protein / Domain of Unknown Function / Novel Fold / Micro-ED

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