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TitleFragment-Based Phasing of Peptidic Nanocrystals by MicroED.
Journal, issue, pagesACS Bio Med Chem Au, Vol. 3, Issue 2, Page 201-210, Year 2023
Publish dateApr 19, 2023
AuthorsLogan S Richards / Maria D Flores / Claudia Millán / Calina Glynn / Chih-Te Zee / Michael R Sawaya / Marcus Gallagher-Jones / Rafael J Borges / Isabel Usón / Jose A Rodriguez /
PubMed AbstractElectron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic ...Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
External linksACS Bio Med Chem Au / PubMed:37096030 / PubMed Central
MethodsEM (electron crystallography) / X-ray diffraction
Resolution0.9 - 1.503 Å
Structure data

PDB-7n2d:
MicroED structure of human zinc finger protein 292 segment (534-542) phased by ARCIMBOLDO-BORGES
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.503 Å

PDB-7n2e:
MicroED structure of human CPEB3 segment (154-161) straight polymorph
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.0 Å

PDB-7n2f:
MicroED structure of human CPEB3 segment (154-161) straight polymorph phased by ARCIMBOLDO-BORGES
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.2 Å

PDB-7n2g:
MicroED structure of human CPEB3 segment(154-161) kinked polymorph phased by ARCIMBOLDO-BORGES
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.201 Å

PDB-7n2h:
X-Ray structure of a sequence variant of a repeat segment of the yeast prion New1p
Method: X-RAY DIFFRACTION / Resolution: 1.102 Å

PDB-7n2i:
MicroED structure of human LECT2 (45-53) phased by ARCIMBOLDO-BORGES
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.402 Å

PDB-7n2j:
MicroED structure of a mutant mammalian prion segment phased by ARCIMBOLDO-BORGES
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.5 Å

PDB-7n2k:
MicroED structure of sequence variant of repeat segment of the yeast prion New1p phased by ARCIMBOLDO-BORGES
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.301 Å

PDB-7n2l:
MicroED structure of a mutant mammalian prion segment
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 0.9 Å

Chemicals

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • saccharomyces cerevisiae (brewer's yeast)
  • synthetic construct (others)
KeywordsPROTEIN FIBRIL / amyloid / MicroED / zinc finger / phasing / functional amyloid / prion / New1p / LECT2 / yeast

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