Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM.
GroEL
MrBUMP
cryo-EM
molecular replacement
Journal
Acta crystallographica. Section D, Structural biology
ISSN: 2059-7983
Titre abrégé: Acta Crystallogr D Struct Biol
Pays: United States
ID NLM: 101676043
Informations de publication
Date de publication:
01 Nov 2021
01 Nov 2021
Historique:
received:
07
04
2021
accepted:
03
09
2021
entrez:
2
11
2021
pubmed:
3
11
2021
medline:
11
2
2022
Statut:
ppublish
Résumé
In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (<8 Å) data sets.
Identifiants
pubmed: 34726166
pii: S2059798321009165
doi: 10.1107/S2059798321009165
pmc: PMC8561737
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1378-1385Subventions
Organisme : Medical Research Council
ID : MR/N009614/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/V000403/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S007105/1
Pays : United Kingdom
Informations de copyright
open access.
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