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TitleA microtubule RELION-based pipeline for cryo-EM image processing.
Journal, issue, pagesJ Struct Biol, Vol. 209, Issue 1, Page 107402, Year 2020
Publish dateJan 1, 2020
AuthorsAlexander D Cook / Szymon W Manka / Su Wang / Carolyn A Moores / Joseph Atherton /
PubMed AbstractMicrotubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall ...Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.
External linksJ Struct Biol / PubMed:31610239 / PubMed Central
MethodsEM (single particle) / EM (helical sym.)
Resolution3.8 - 4.5 Å
Structure data

EMDB-10131:
MKLP2-decocrated 13 protofilament microtubule (ADP.Al.Fx state) processed with MiRP (Microtubule Relion-based Pipeline)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-10195:
Doublecortin N-terminal DC-domain (NDC)-decorated 13-protofilament microtubule (GDP state) processed with MiRP (Microtubule Relion-based Pipeline)
Method: EM (helical sym.) / Resolution: 4.5 Å

4862

6rf8

EMDB-4862, PDB-6rf8:
Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

ChemComp-MG:
Unknown entry

Source
  • bos taurus (cattle)
  • Mus musculus (house mouse)
  • homo sapiens (human)
KeywordsCYTOSOLIC PROTEIN / Microtubule-associated protein / neuronal migration protein / ubiquitin-like fold / microtubule nucleation and stabilisation

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