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- EMDB-15451: Sub-tomogram average of TAILS in bovine sperm tail tip singlet mi... -

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Basic information

Entry
Database: EMDB / ID: EMD-15451
TitleSub-tomogram average of TAILS in bovine sperm tail tip singlet microtubules.
Map data
Sample
  • Complex: SPACA9 inner microtubule decoration.
KeywordsMicrotubules Flagella Bovine Sperm / UNKNOWN FUNCTION
Biological speciesBos taurus (cattle)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsZabeo D / Hoog JL
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2019-04004 Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.
Authors: Miao Gui / Jacob T Croft / Davide Zabeo / Vajradhar Acharya / Justin M Kollman / Thomas Burgoyne / Johanna L Höög / Alan Brown /
Abstract: 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 ...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.
History
DepositionJul 22, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15451.png

Downloads & links

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Map

FileDownload / File: emd_15451.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.37 Å/pix.
x 100 pix.
= 437. Å		4.37 Å/pix.
x 100 pix.
= 437. Å		4.37 Å/pix.
x 100 pix.
= 437. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 175.0
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)132.434079999999994 (±27.606949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 437.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15451_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_15451_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : SPACA9 inner microtubule decoration.

EntireName: SPACA9 inner microtubule decoration.
Components
  • Complex: SPACA9 inner microtubule decoration.

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Supramolecule #1: SPACA9 inner microtubule decoration.

SupramoleculeName: SPACA9 inner microtubule decoration. / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (cattle) / Tissue: Sperm / Organelle: Flagellum

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.64 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: PEET / Number subtomograms used: 14549
ExtractionNumber tomograms: 10 / Number images used: 14549 / Software - Name: PEET
Final angle assignmentType: NOT APPLICABLE / Software - Name: PEET

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