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- EMDB-50873: 96-nm repeat of axonemal doublet microtubules from bovine sperm, ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-50873
Title96-nm repeat of axonemal doublet microtubules from bovine sperm, RS3 stalk local refinement
Map datasharpened map
Sample
  • Organelle or cellular component: 96-nm repeat of axonemal doublet microtubules from bovine sperm
Keywordsaxoneme / cilia / microtubule / dynein / sperm / STRUCTURAL PROTEIN
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLeung MR / Sun C / Zeng J / Anderson JR / Niu Q / Huang W / Noteborn WEM / Brown A / Zeev-Ben-Mordehai T / Zhang R
Funding support Netherlands, United States, 4 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.XL21.XL21.048 Netherlands
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM143183 United States
CitationJournal: To Be Published
Title: Structural diversity of axonemes across mammalian motile cilia
Authors: Leung MR / Sun C / Zeng J / Anderson JR / Niu Q / Huang W / Noteborn WEM / Brown A / Zeev-Ben-Mordehai T / Zhang R
History
DepositionJul 3, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50873.png

Downloads & links

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Map

FileDownload / File: emd_50873.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 512 pix.
= 666.214 Å		1.3 Å/pix.
x 512 pix.
= 666.214 Å		1.3 Å/pix.
x 512 pix.
= 666.214 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3012 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0067038047 - 2.4293537
Average (Standard dev.)0.0011071636 (±0.020091403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 666.2144 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 96-nm repeat of axonemal doublet microtubules from bovine sperm

EntireName: 96-nm repeat of axonemal doublet microtubules from bovine sperm
Components
  • Organelle or cellular component: 96-nm repeat of axonemal doublet microtubules from bovine sperm

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Supramolecule #1: 96-nm repeat of axonemal doublet microtubules from bovine sperm

SupramoleculeName: 96-nm repeat of axonemal doublet microtubules from bovine sperm
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#479
Source (natural)Organism: Bos taurus (cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2585140
Startup modelType of model: EMDB MAP
EMDB ID:

24664

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 203560
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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