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- EMDB-20633: Composite cryo-EM density map of half 2 of the 96-nm repeat of th... -

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Basic information

Entry
Database: EMDB / ID: EMD-20633
TitleComposite cryo-EM density map of half 2 of the 96-nm repeat of the doublet microtubule from wild-type Chlamydomonas reinhardtii
Map dataComposite cryo-EM density map of half 2 of the 96-nm repeat of the doublet microtubule from wild-type Chlamydomonas reinhardtii
Sample
  • Complex: doublet microtubule from wild-type Chlamydomonas reinhardtii
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsMa M / Stoyanova M / Rademacher G / Dutcher SK / Brown A / Zhang R
CitationJournal: Cell / Year: 2019
Title: Structure of the Decorated Ciliary Doublet Microtubule.
Authors: Meisheng Ma / Mihaela Stoyanova / Griffin Rademacher / Susan K Dutcher / Alan Brown / Rui Zhang /
Abstract: The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility ...The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility require a radially arranged set of doublet microtubules, each decorated in repeating patterns with non-tubulin components. We use single-particle cryo-electron microscopy to visualize and build an atomic model of the repeating structure of a native axonemal doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). The structure demonstrates how these proteins establish the unique architecture of doublet microtubules, maintain coherent periodicities along the axoneme, and stabilize the microtubules against the repeated mechanical stress induced by ciliary motility. Our work elucidates the architectural principles that underpin the assembly of this large, repetitive eukaryotic structure and provides a molecular basis for understanding the etiology of human ciliopathies.
History
DepositionAug 22, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20633.png

Downloads & links

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Map

FileDownload / File: emd_20633.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite cryo-EM density map of half 2 of the 96-nm repeat of the doublet microtubule from wild-type Chlamydomonas reinhardtii
Voxel sizeX=Y=Z: 1.403 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.041636262 - 0.10757877
Average (Standard dev.)0.0016466767 (±0.0062426412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 718.336 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z718.336718.336718.336
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0420.1080.002

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Supplemental data

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Mask #1

Fileemd_20633_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 of the composite cryo-EM density...

Fileemd_20633_half_map_1.map
Annotationhalf map 1 of the composite cryo-EM density map of half 2 of the 96-nm repeat of the doublet microtubule from wild-type Chlamydomonas reinhardtii
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 of the composite cryo-EM density...

Fileemd_20633_half_map_2.map
Annotationhalf map 2 of the composite cryo-EM density map of half 2 of the 96-nm repeat of the doublet microtubule from wild-type Chlamydomonas reinhardtii
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : doublet microtubule from wild-type Chlamydomonas reinhardtii

EntireName: doublet microtubule from wild-type Chlamydomonas reinhardtii
Components
  • Complex: doublet microtubule from wild-type Chlamydomonas reinhardtii

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Supramolecule #1: doublet microtubule from wild-type Chlamydomonas reinhardtii

SupramoleculeName: doublet microtubule from wild-type Chlamydomonas reinhardtii
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-125

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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 / Component - Name: HMDEKP
Details: 30 mM HEPES, 5 mM MgSO4, 1 mM DTT, 0.5 mM EGTA, 25 mM KCl, PH 7.4
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.1 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 81000
Specialist opticsSpherical aberration corrector: Microscope is equipped with a Cs corrector
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 6 / Number real images: 8314 / Average exposure time: 9.0 sec. / Average electron dose: 38.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: doublet microtubules were manually selected
CTF correctionSoftware: (Name: RELION, Gctf)
Details: CTF parameters were estimated using Gctf and corrected during 3D reconstruction within RELION
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 300
Projection matching processing - Angular sampling: 4.0 degrees
Software - Name: EMAN
Final 3D classificationNumber classes: 6 / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 112000
DetailsThe movies were drift-corrected using UCSF MotionCorr2
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 50

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