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- EMDB-24663: Cryo-EM density map of the outer dynein arm core from bovine trac... -

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Basic information

Entry
Database: EMDB / ID: EMD-24663
TitleCryo-EM density map of the outer dynein arm core from bovine tracheal cilia
Map data
Sample
  • Complex: Outer dynein arm bound to doublet microtubule
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsGui M / Anderson JR / Botsch JJ / Meleppattu S / Singh SK / Zhang Q / Brown A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell / Year: 2021
Title: De novo identification of mammalian ciliary motility proteins using cryo-EM.
Authors: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James ...Authors: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James Thompson / Jane S Lucas / Colin D Bingle / Dominic P Norris / Sudipto Roy / Alan Brown /
Abstract: Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner ...Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility.
History
DepositionAug 10, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24663.png

Downloads & links

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Map

FileDownload / File: emd_24663.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.003 / Movie #1: 0.004
Minimum - Maximum-0.010498769 - 0.019279432
Average (Standard dev.)4.639217e-05 (±0.0007617209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 488.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z488.320488.320488.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0100.0190.000

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Supplemental data

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Mask #1

Fileemd_24663_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24663_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_24663_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 : Outer dynein arm bound to doublet microtubule

EntireName: Outer dynein arm bound to doublet microtubule
Components
  • Complex: Outer dynein arm bound to doublet microtubule

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Supramolecule #1: Outer dynein arm bound to doublet microtubule

SupramoleculeName: Outer dynein arm bound to doublet microtubule / type: complex / ID: 1 / Parent: 0
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: 1267170
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

20631

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 8755
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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