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- EMDB-45701: Dynein motor inner dynein arm subform f (IDAf) from Porcine brain... -

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Basic information

Entry
Database: EMDB / ID: EMD-45701
TitleDynein motor inner dynein arm subform f (IDAf) from Porcine brain ventricles
Map data
Sample
  • Organelle or cellular component: cilia from Porcine brain ventricles
Keywordsaxoneme / cilia / microtubule / dynein / brain ventricle / doublet microtubule (DMT) / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.55 Å
AuthorsSun C / Zhang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 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 11, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45701.png

Downloads & links

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Map

FileDownload / File: emd_45701.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 512 pix.
= 686.08 Å		1.34 Å/pix.
x 512 pix.
= 686.08 Å		1.34 Å/pix.
x 512 pix.
= 686.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3510536 - 0.5569172
Average (Standard dev.)0.002258323 (±0.023701575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 686.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45701_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45701_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45701_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cilia from Porcine brain ventricles

EntireName: cilia from Porcine brain ventricles
Components
  • Organelle or cellular component: cilia from Porcine brain ventricles

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Supramolecule #1: cilia from Porcine brain ventricles

SupramoleculeName: cilia from Porcine brain ventricles / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

40619

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18428
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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