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Structure paper

TitleA cryo-EM processing pipeline for microtubules using CryoSPARC.
Journal, issue, pagesActa Crystallogr D Struct Biol, Vol. 82, Issue Pt 5, Page 411-420, Year 2026
Publish dateMay 1, 2026
AuthorsDaniel Zhang / Hugo Muñoz-Hernández / Pavel Filipcik / Kushal Sejwal / Yixin Xu / Sung Ryul Choi / Michel O Steinmetz / Michal Wieczorek /
PubMed AbstractMicrotubules are cytoskeletal filaments that are typically characterized by a discontinuous helical lattice of α/β-tubulin heterodimers. Microtubules can also adopt variable lattice architectures ...Microtubules are cytoskeletal filaments that are typically characterized by a discontinuous helical lattice of α/β-tubulin heterodimers. Microtubules can also adopt variable lattice architectures both in vitro and in cellular contexts. Pseudo-helical averaging processing strategies have been developed to generate cryo-EM reconstructions of microtubules with and without decorating protein-binding partners, but these pipelines can be difficult to implement for the average user, especially for undecorated filaments. Here, we describe MiCSPARC, a cryo-EM processing pipeline developed around CryoSPARC [Punjani et al. (2017), Nat. Methods, 14, 290-296], which leverages automated particle picking and fast 3D refinement times in CryoSPARC to determine the structures of both decorated and undecorated microtubules. We generate reconstructions of undecorated GDP microtubules, as well as kinesin-1 motor domain-decorated GMPCPP filaments, at resolutions of up to 2.8 Å, demonstrating the robustness of the pipeline. Based on its convenient implementation and its ability to routinely generate high-resolution, seam-corrected microtubule reconstructions, MiCSPARC should provide a valuable tool for understanding microtubule dynamics, microtubule-associated proteins and microtubule-targeting agents.
External linksActa Crystallogr D Struct Biol / PubMed:42044018 / PubMed Central
MethodsEM (single particle)
Resolution2.77 - 4.16 Å
Structure data

55425

9t17

EMDB-55425, PDB-9t17:
Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule
Method: EM (single particle) / Resolution: 2.77 Å

55431

9t1d

EMDB-55431, PDB-9t1d:
Cryo-EM reconstruction of undecorated GDP microtubule
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55440: Cryo-EM reconstruction of undecorated GDP microtubule (13-3)
Method: EM (single particle) / Resolution: 3.62 Å

EMDB-55444: Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule (14-3)
Method: EM (single particle) / Resolution: 4.16 Å

Chemicals

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

ChemComp-MG:
Unknown entry

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

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

Source
  • bos taurus (domestic cattle)
  • homo sapiens (human)
  • sus scrofa (pig)
KeywordsSTRUCTURAL PROTEIN / Microtubule-binding motor domain. Tubulin dimer. / Microtubule. Tubulin dimer.

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