basal body cartwheel inner density

cellstructuremech:basal_body_cartwheel_inner_density · Cytoskeleton · Other · Proposed

A morphologically distinct subassembly within the lumen of a microbial basal-body cartwheel hub, observed as a central electron-dense unit separate from the surrounding hub rings and radial spokes. Such units can repeat along the cartwheel axis, with nonuniform occupancy. [DOI:10.15252/embj.2020106246]

Synonyms: cartwheel inner density; CID; centriole cartwheel inner density

Part of: basal body cartwheel (cellstructuremech:basal_body_cartwheel)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Canonical examples

• NCBITaxon:3055 Chlamydomonas reinhardtii — In-situ cryo-FIB/cryo-ET of mat3-4 cells resolves CIDs within the hubs of mature basal bodies and pro-basal bodies. Figure 1 distinguishes the inner densities from the surrounding hub. The Results paragraph discussing the Figure 3 reconstruction also reports raw regions without CID, citing Appendix Figure S4D. [DOI:10.15252/embj.2020106246]
• NCBITaxon:5888 Paramecium tetraurelia — Cryo-ET of isolated cortical units and cartwheel averaging resolve CIDs in Figures 2 and 3. Preparation used d4-2 and Delta-CenBP1 strains; the cited figure is not assigned to one strain. These are native specimens, not recombinant SAS-6 rings. [DOI:10.15252/embj.2020106246]
• NCBITaxon:5762 Naegleria gruberi — Basal bodies isolated from NEG cells differentiated into flagellates show CIDs in Figure 2 and Figure EV2. Periodicities were assessed in undamaged regions because preparation often compressed the basal bodies. This does not assert CID presence in the amoeboid stage. [DOI:10.15252/embj.2020106246]
• NCBITaxon:63628 Trichonympha agilis — Purified basal bodies from flagellates extracted from Reticulitermes speratus hindguts were examined by cryo-ET and subtomogram averaging. Figure 2F-J and Figure EV1 describe 55% and 45% subvolume classes that can occur within one basal body, not separate taxa or population prevalence estimates. [DOI:10.15252/embj.2020106249]

Physical properties

• OTHER: 8.7 +/- 1.6 UO:0000018 (Axial spacing between CIDs in mature Chlamydomonas reinhardtii basal bodies imaged in situ in mat3-4 cells; Klena Figure 1, plotted in panel H of the original graphic. Mean and SD, n=18 measured distances, not 18 cells or protein copies. This is not CID diameter, hub-ring spacing, or a universal repeat.) [DOI:10.15252/embj.2020106246]
• OTHER: 8.6 +/- 1.2 UO:0000018 (Axial CID spacing in Chlamydomonas reinhardtii pro-basal bodies in the same in-situ mat3-4 study; Klena Figure 1. Mean and SD, n=5 measured distances. Mature and pro-basal-body measurements are separate observations, not a time course or a demonstrated developmental change.) [DOI:10.15252/embj.2020106246]
• OTHER: 8.3 +/- 0.5 UO:0000018 (Axial spacing between CID elements in the Trichonympha agilis 55% central-cartwheel subvolume class, Nazarov Figure 2H. Reported mean and error; the caption does not name the error statistic. N=9 denotes 2D measurements from the subtomogram average, not independent cells. The 55% is a reconstruction-class fraction, not biological occupancy.) [DOI:10.15252/embj.2020106249]
• OTHER: 15.2 UO:0000018 (Distance between two CID elements in the Trichonympha agilis 45% central-cartwheel class, Nazarov Figure EV1C; N=1 2D measurement from the subtomogram average, with no error estimate. An intervening single hub unit lacks a neighboring CID. This is not a species-wide mean or a second universal repeat.) [DOI:10.15252/embj.2020106249]

Discussions

• CURATION_TODO (RESOLVED): Keep the named inner-density subassembly distinct from the cartwheel hub and its proteins. A density-defined cellular subassembly is not a protein assignment, and the CID abbreviation has been used at two levels of granularity.
• CURATION_TODO (OPEN): Identify native microbial CID constituents and test CID-specific biological roles. Morphological contacts and structural models do not demonstrate a protein identity, necessity, or causal mechanism.
• CURATION_TODO (RESOLVED): Do not transfer SAS-6 hub assignments or speculative fly Poc1B assignments into microbial CID composition. A surrounding hub protein and a proposed analogous host structure do not identify this microbial subassembly.
• CURATION_TODO (OPEN): Resolve whether discrete CID and filamentous CID share molecular identity or homology. A similar location does not establish equivalence of discontinuous central units and a continuous axial filament.
• CURATION_TODO (OPEN): Reconcile class- and reference-frame-specific CID polarity without imposing universal occupancy. Different sample preparations, resolution limits and geometric reference axes can produce distinct observations.
• CURATION_TODO (OPEN): Inspect the full 2026 Trichonympha study before extending molecular or mechanistic claims. An abstract and deposited hub model cannot substitute for Results and Methods or identify an unmodeled density.
• CURATION_TODO (RESOLVED): Keep CID spacing, hub architecture, reconstruction processing and taxonomic scope separate. Image labels, symmetry processing and measurement counts are not interchangeable with molecular or population evidence.

Datasets

• Trichonympha agilis central cartwheel without variations, 55% class (EMDB:EMD-10916) · OTHER · STRUCTURAL_IMAGING
  Organism: Trichonympha agilis · Platform: cryo-electron tomography and subtomogram averaging

  Native metadata verifies released status, the 55% title, taxon 63628, DOI and PMID:32954505. Metadata and links only; no map volume downloaded and no exact CID xref asserted.

• Trichonympha agilis central cartwheel with variations, 45% class (EMDB:EMD-10918) · OTHER · STRUCTURAL_IMAGING
  Organism: Trichonympha agilis · Platform: cryo-electron tomography and subtomogram averaging

  Native metadata verifies released status, the 45% title, taxon 63628, DOI and PMID:32954505. No map volume downloaded or exact structure xref asserted. Percentages describe classified subvolumes, not fractions of organisms.

Evidence

• DOI:10.15252/embj.2020106246 Klena et al. 2020, PMID:32954513. Checksum-verified PMC7667884.1 Introduction, CID Results, figure captions, Discussion and specimen/averaging Methods inspected. Original Figure 1 visually inspected. Supports named inner-density identity and native microbial examples, not molecular composition or a proven CID-specific mechanism.
• DOI:10.15252/embj.2020106249 Nazarov et al. 2020, PMID:32954505. Checksum-verified PMC7667878.1 Results, Figure 2 and Figure EV1 captions, Discussion and specimen preparation inspected. Distinguishes the discrete CID, variable cartwheel classes, and the potentially related filamentous form; proposed symmetry and polarity roles are not treated as experimental functions.

Curation history

• 2026-10-04T16:37:12Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
• 2026-10-04T16:39:15Z codex · CURATED_RECORD — Added four native microbial CID examples, scoped axial spacings, distinct reconstruction classes and an inspected unmodified CC BY figure. Defined whole-CID granularity and cartwheel parthood; preserved uncertain composition, functions, polarity and filamentous-form homology. Declined unsupported hub-protein and speculative host Poc1B assignments and documented the unread newer full-text boundary.
• 2026-10-04T16:40:25Z codex · CURATED_RECORD — Refined the Chlamydomonas occupancy source pointer to the inspected Results paragraph and its Appendix Figure S4D citation.

Source: data/structures/cytoskeleton/basal_body_cartwheel_inner_density.yaml