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- EMDB-26210: Barb-like structure on the external surface of the Salpingoeca ro... -

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Basic information

Entry
Database: EMDB / ID: EMD-26210
TitleBarb-like structure on the external surface of the Salpingoeca rosetta (choanoflagellate) ciliary membrane
Map dataBarb-like structure on the external surface of the Salpingoeca rosetta (choanoflagellate) ciliary membrane
Sample
  • Organelle or cellular component: barb structure from Salpingoeca rosetta ciliary membrane
Keywordscilia membrane-associated barb / UNKNOWN FUNCTION
Biological speciesSalpingoeca rosetta (eukaryote)
Methodelectron tomography / cryo EM
AuthorsPinskey JM / Nicastro D
Funding support United States, 4 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM083122 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM137470 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140082 United States
CitationJournal: Elife / Year: 2022
Title: Barb-like structure on the external surface of the Salpingoeca rosetta (choanoflagellate) ciliary membrane, generated via cryo-electron tomography and subtomogram averaging.
Authors: Pinskey JM / Nicastro D
History
DepositionFeb 15, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26210.png

Downloads & links

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Map

FileDownload / File: emd_26210.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBarb-like structure on the external surface of the Salpingoeca rosetta (choanoflagellate) ciliary membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.15 Å/pix.
x 240 pix.
= 756.24 Å		3.15 Å/pix.
x 240 pix.
= 756.24 Å		3.15 Å/pix.
x 240 pix.
= 756.24 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.151 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum121.555710000000005 - 137.434050000000013
Average (Standard dev.)127.320830000000001 (±1.3384804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 756.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : barb structure from Salpingoeca rosetta ciliary membrane

EntireName: barb structure from Salpingoeca rosetta ciliary membrane
Components
  • Organelle or cellular component: barb structure from Salpingoeca rosetta ciliary membrane

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Supramolecule #1: barb structure from Salpingoeca rosetta ciliary membrane

SupramoleculeName: barb structure from Salpingoeca rosetta ciliary membrane
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Molecular complex of unknown function that protrudes from the external surface of the ciliary membrane
Source (natural)Organism: Salpingoeca rosetta (eukaryote) / Location in cell: cilium

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
Cryo protectantliquid ethane
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Millipore Sigma / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionDetails: 4-fold symmetry / Number images used: 61

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