Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Richards, Logan S.; Millán, Claudia; Miao, Jennifer; Martynowycz, Michael W.; Sawaya, Michael R.; Gonen, Tamir; Borges, Rafael J.; Usón, Isabel; Rodriguez, Jose A.

doi:10.1107/S2059798320008049

Title: Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Journal Article · Mon Jul 27 00:00:00 EDT 2020 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798320008049· OSTI ID:1643203

Richards, Logan S.; Millán, Claudia; Miao, Jennifer; Martynowycz, Michael W.; Sawaya, Michael R.; Gonen, Tamir; Borges, Rafael J.; Usón, Isabel; Rodriguez, Jose A.

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

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Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); NIH–NIGMS

Grant/Contract Number:: FC02-02ER63421; R35 GM128867; P41GM136508

OSTI ID:: 1643203

Alternate ID(s):: OSTI ID: 1799621

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Vol. 76 Journal Issue: 8; ISSN 2059-7983

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
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Crystallography
phasing
crystal
fragment
electron diffraction
cryoEM
MicroED
proteinase K
ARCIMBOLDO_SHREDDER

Title: Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

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