6RF8

Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule

Summary for 6RF8

• Entry DOI: 10.2210/pdb6rf8/pdb
• EMDB information: 4862
• Descriptor: Neuronal migration protein doublecortin, Tubulin beta-2B chain, Tubulin alpha-1B chain, ... (6 entities in total)
• Functional Keywords: microtubule-associated protein, neuronal migration protein, ubiquitin-like fold, microtubule nucleation and stabilisation, cytosolic protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 5
• Total formula weight: 206176.65

Authors

Manka, S.W. (deposition date: 2019-04-12, release date: 2020-04-15, Last modification date: 2024-05-22)

Primary citation

Cook, A.D.,Manka, S.W.,Wang, S.,Moores, C.A.,Atherton, J.
A microtubule RELION-based pipeline for cryo-EM image processing.
J.Struct.Biol., 209:107402-107402, 2020

PubMed Abstract: 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.

PubMed: 31610239
DOI: 10.1016/j.jsb.2019.10.004

Experimental method

ELECTRON MICROSCOPY (3.8 Å)