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- EMDB-10896: First cryo-ET / subtomogram averaging of primary cilia microtubul... -

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Basic information

Entry
Database: EMDB / ID: EMD-10896
TitleFirst cryo-ET / subtomogram averaging of primary cilia microtubules show that A-tubules are decorated by EB1
Map dataSubtomogram average of EB1 decorated A-microtubule from MDCKII primary cilia axonemes
Sample
  • Complex: Subtomogram average of EB1 decorated A-microtubule from cryo-tomograms of MDCKII primary cilia
Biological speciesCanis lupus familiaris (dog)
Methodsubtomogram averaging / cryo EM / Resolution: 18.56 Å
AuthorsKiesel P / Alvarez Viar G / Tsoy N / Maraspini R / Honigmann A / Pigino G
Funding support1 items
OrganizationGrant numberCountry
European Research Council (ERC)819826
Citation
Journal: Nat Struct Mol Biol / Year: 2020
Title: The molecular structure of mammalian primary cilia revealed by cryo-electron tomography.
Authors: Petra Kiesel / Gonzalo Alvarez Viar / Nikolai Tsoy / Riccardo Maraspini / Peter Gorilak / Vladimir Varga / Alf Honigmann / Gaia Pigino /
Abstract: Primary cilia are microtubule-based organelles that are important for signaling and sensing in eukaryotic cells. Unlike the thoroughly studied motile cilia, the three-dimensional architecture and ...Primary cilia are microtubule-based organelles that are important for signaling and sensing in eukaryotic cells. Unlike the thoroughly studied motile cilia, the three-dimensional architecture and molecular composition of primary cilia are largely unexplored. Yet, studying these aspects is necessary to understand how primary cilia function in health and disease. We developed an enabling method for investigating the structure of primary cilia isolated from MDCK-II cells at molecular resolution by cryo-electron tomography. We show that the textbook '9 + 0' arrangement of microtubule doublets is only present at the primary cilium base. A few microns out, the architecture changes into an unstructured bundle of EB1-decorated microtubules and actin filaments, putting an end to a long debate on the presence or absence of actin filaments in primary cilia. Our work provides a plethora of insights into the molecular structure of primary cilia and offers a methodological framework to study these important organelles.
#1: Journal: Biorxiv / Year: 2020
Title: The molecular structure of primary cilia revealed by cryo-electron tomography
Authors: Kiesel P / Alvarez Viar G / Tsoy N / Maraspini R / Honigmann A / Pigino G
History
DepositionApr 22, 2020-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10896.png

Downloads & links

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Map

FileDownload / File: emd_10896.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of EB1 decorated A-microtubule from MDCKII primary cilia axonemes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.71 Å/pix.
x 70 pix.
= 329.77 Å		4.71 Å/pix.
x 160 pix.
= 753.76 Å		4.71 Å/pix.
x 70 pix.
= 329.77 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.711 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.15 / Movie #1: 2.15
Minimum - Maximum-4.494527 - 4.508195
Average (Standard dev.)-0.0012947011 (±1.4729619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1607070
Spacing7016070
CellA: 329.77 Å / B: 753.76 Å / C: 329.77 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.7114.7114.711
M x/y/z7016070
origin x/y/z0.0000.0000.000
length x/y/z329.770753.760329.770
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS7016070
D min/max/mean-4.4954.508-0.001

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Supplemental data

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Sample components

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Entire : Subtomogram average of EB1 decorated A-microtubule from cryo-tomo...

EntireName: Subtomogram average of EB1 decorated A-microtubule from cryo-tomograms of MDCKII primary cilia
Components
  • Complex: Subtomogram average of EB1 decorated A-microtubule from cryo-tomograms of MDCKII primary cilia

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Supramolecule #1: Subtomogram average of EB1 decorated A-microtubule from cryo-tomo...

SupramoleculeName: Subtomogram average of EB1 decorated A-microtubule from cryo-tomograms of MDCKII primary cilia
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Canis lupus familiaris (dog) / Organ: Kidney / Tissue: tubule epithelial tissue / Organelle: primary cilium / Location in cell: axoneme

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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: 7.25
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 2970
ExtractionNumber tomograms: 10 / Number images used: 2970
CTF correctionSoftware - Name: CTFPHASEFLIP
Final angle assignmentType: OTHER
Crystal parametersUnit cell - A: 1 Å / Unit cell - B: 1 Å / Unit cell - C: 1 Å / Unit cell - γ: 1 ° / Unit cell - α: 1 ° / Unit cell - β: 1 ° / Space group: 1

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