SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules

Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2207605119. doi: 10.1073/pnas.2207605119. Epub 2022 Oct 3.


The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients.

Keywords: axoneme; cilia; cryo-EM; cryo-ET; microtubules.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Axoneme / metabolism
  • Ciliopathies* / metabolism
  • Cryoelectron Microscopy
  • Humans
  • Male
  • Microtubule Proteins / chemistry
  • Microtubule Proteins / genetics
  • Microtubules / metabolism
  • Proteins
  • Semen* / metabolism


  • Microtubule Proteins
  • Proteins
  • SPACA9 protein, human