7SKX

Ab initio structure of proteinase K from electron-counted MicroED data

Summary for 7SKX

• Entry DOI: 10.2210/pdb7skx/pdb
• EMDB information: 25184 25185
• Descriptor: Proteinase K, 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: hydrolase
• Biological source: Parengyodontium album (Engyodontium album, Tritirachium album)
• Total number of polymer chains: 1
• Total formula weight: 30248.84

Authors

Martynowycz, M.W.,Clabbers, M.T.B.,Hattne, J.,Gonen, T. (deposition date: 2021-10-21, release date: 2022-06-08, Last modification date: 2024-10-16)

Primary citation

Martynowycz, M.W.,Clabbers, M.T.B.,Hattne, J.,Gonen, T.
Ab initio phasing macromolecular structures using electron-counted MicroED data.
Nat.Methods, 19:724-729, 2022

PubMed Abstract: Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.

PubMed: 35637302
DOI: 10.1038/s41592-022-01485-4

Experimental method

ELECTRON CRYSTALLOGRAPHY (1.5 Å)