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TitleQuantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates.
Journal, issue, pagesStructure, Vol. 30, Issue 4, Page 498-509.e4, Year 2022
Publish dateApr 7, 2022
AuthorsJessica N Rabuck-Gibbons / Dmitry Lyumkis / James R Williamson /
PubMed AbstractSingle-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations ...Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations into different groups through computational classification. However, there is a dearth of tools for surveying the heterogeneity landscape, quantitatively analyzing heterogeneous particle populations after classification, deciding how many unique classes are represented by the data, and accurately cross-comparing reconstructions. Here, we develop a workflow that contains discovery and analysis modules to quantitatively mine cryo-EM data for sets of structures with maximal diversity. This workflow was applied to a dataset of E. coli 50S ribosome assembly intermediates, which are characterized by significant structural heterogeneity. We identified more detailed branchpoints in the assembly process and characterized the interactions of an assembly factor with immature intermediates. While the tools described here were developed for ribosome assembly, they should be broadly applicable to the analysis of other heterogeneous cryo-EM datasets.
External linksStructure / PubMed:34990602 / PubMed Central
MethodsEM (single particle)
Resolution4.5 - 13.6 Å
Structure data

EMDB-24491:
bL17-depleted large ribosome assembly intermediate #20
Method: EM (single particle) / Resolution: 7.9 Å

EMDB-24492:
E. coli bL17-limitation ribosome assembly intermediate #16
Method: EM (single particle) / Resolution: 7.1 Å

EMDB-24499:
E. coli bL17-limitation ribosome assembly intermediate #15
Method: EM (single particle) / Resolution: 7.0 Å

EMDB-24508:
E. coli bL17-limitation ribosome assembly intermediate #17
Method: EM (single particle) / Resolution: 8.7 Å

EMDB-24509:
E. coli bL17-limitation ribosome assembly intermediate #27
Method: EM (single particle) / Resolution: 6.6 Å

EMDB-24510:
E. coli bL17-limitation ribosome assembly intermediate #9
Method: EM (single particle) / Resolution: 7.4 Å

EMDB-24515:
E. coli bL17-limitation ribosome assembly intermediate #8
Method: EM (single particle) / Resolution: 7.6 Å

EMDB-24517:
E. coli bL17-limitation ribosome assembly intermediate #21
Method: EM (single particle) / Resolution: 5.4 Å

EMDB-24520:
E. coli bL17-limitation ribosome assembly intermediate #23
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-24521:
E. coli bL17-limitation ribosome assembly intermediate #22
Method: EM (single particle) / Resolution: 7.1 Å

EMDB-24527:
E. coli bL17-limitation ribosome assembly intermediate #40
Method: EM (single particle) / Resolution: 8.6 Å

EMDB-24538:
E. coli bL17-limitation ribosome assembly intermediate #35
Method: EM (single particle) / Resolution: 10.25 Å

EMDB-24539:
E. coli bL17-limitation ribosome assembly intermediate #39
Method: EM (single particle) / Resolution: 10.08 Å

EMDB-24543:
E. coli bL17-limitation ribosome assembly intermediate #37
Method: EM (single particle) / Resolution: 8.3 Å

EMDB-24546:
E. coli bL17-limitation ribosome assembly intermediate #38
Method: EM (single particle) / Resolution: 8.5 Å

EMDB-24550:
E. coli bL17-limitation ribosome assembly intermediate #41
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-24555:
E. coli bL17-limitation ribosome assembly intermediate #41
Method: EM (single particle) / Resolution: 8.9 Å

EMDB-24558:
E. coli bL17-limitation ribosome assembly intermediate #19
Method: EM (single particle) / Resolution: 9.2 Å

EMDB-24559:
E. coli bL17-limitation ribosome assembly intermediate #18
Method: EM (single particle) / Resolution: 6.6 Å

EMDB-24561:
E. coli bL17-limitation ribosome assembly intermediate #28
Method: EM (single particle) / Resolution: 4.9 Å

EMDB-24562:
E. coli bL17-limitation ribosome assembly intermediate #29
Method: EM (single particle) / Resolution: 6.1 Å

EMDB-24563:
E. coli bL17-limitation ribosome assembly intermediate #25
Method: EM (single particle) / Resolution: 5.7 Å

EMDB-24564:
E. coli bL17-limitation ribosome assembly intermediate #26
Method: EM (single particle) / Resolution: 7.0 Å

EMDB-24565:
E. coli bL17-limitation ribosome assembly intermediate #26
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-24567:
E. coli bL17-limitation ribosome assembly intermediate #2
Method: EM (single particle) / Resolution: 13.09 Å

EMDB-24568:
E. coli bL17-limitation ribosome assembly intermediate #3
Method: EM (single particle) / Resolution: 9.8 Å

EMDB-24571:
E. coli bL17-limitation ribosome assembly intermediate #12
Method: EM (single particle) / Resolution: 9.9 Å

EMDB-24573:
E. coli bL17-limitation ribosome assembly intermediate #14
Method: EM (single particle) / Resolution: 11.2 Å

EMDB-24574:
E. coli bL17-limitation ribosome assembly intermediate #13
Method: EM (single particle) / Resolution: 13.6 Å

EMDB-24626:
E. coli bL17-limitation ribosome assembly intermediate #11
Method: EM (single particle) / Resolution: 10.3 Å

EMDB-24627:
E. coli bL17-limitation ribosome assembly intermediate #10
Method: EM (single particle) / Resolution: 9.3 Å

EMDB-24631:
E. coli bL17-limitation ribosome assembly intermediate #4
Method: EM (single particle) / Resolution: 6.3 Å

EMDB-24633:
E. coli bL17-limitation ribosome assembly intermediate #5
Method: EM (single particle) / Resolution: 7.2 Å

EMDB-24634:
E. coli bL17-limitation ribosome assembly intermediate #6
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-24658:
E. coli bL17-limitation ribosome assembly intermediate #7
Method: EM (single particle) / Resolution: 12.3 Å

EMDB-24659:
E. coli bL17-limitation ribosome assembly intermediate #33
Method: EM (single particle) / Resolution: 9.8 Å

EMDB-24660:
E. coli bL17-limitation ribosome assembly intermediate #36
Method: EM (single particle) / Resolution: 10.4 Å

EMDB-24661:
E. coli bL17-limitation ribosome assembly intermediate #34
Method: EM (single particle) / Resolution: 7.1 Å

EMDB-24662:
E. coli bL17-limitation ribosome assembly intermediate #32
Method: EM (single particle) / Resolution: 12.9 Å

EMDB-24669:
E. coli bL17-limitation ribosome assembly intermediate #31
Method: EM (single particle) / Resolution: 8.5 Å

EMDB-24671:
E. coli bL17-limitation ribosome assembly intermediate #1
Method: EM (single particle) / Resolution: 8.9 Å

EMDB-24673:
E. coli bL17-limitation ribosome assembly intermediate #30
Method: EM (single particle) / Resolution: 6.6 Å

Source
  • Escherichia coli (E. coli)

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