- PDB-8t1m: Novel Domain of Unknown Function Solved with AlphaFold -
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Entry
Database: PDB / ID: 8t1m
Title
Novel Domain of Unknown Function Solved with AlphaFold
Components
DUF1842 domain-containing protein
Keywords
UNKNOWN FUNCTION / AlphaFold / Bacterial Protein / Domain of Unknown Function / Novel Fold
Function / homology
Domain of unknown function DUF1842 / Domain of unknown function DUF1843 / Domain of unknown function (DUF1842) / Domain of unknown function (DUF1843) / DUF1842 domain-containing protein
Journal: Acta Crystallogr D Struct Biol / Year: 2024 Title: AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography. Authors: Justin E Miller / Matthew P Agdanowski / Joshua L Dolinsky / Michael R Sawaya / Duilio Cascio / Jose A Rodriguez / Todd O Yeates / 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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