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- EMDB-24419: Microtubule subtomogram average of deconvolved rarticles, randomi... -

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Basic information

Entry
Database: EMDB / ID: EMD-24419
TitleMicrotubule subtomogram average of deconvolved rarticles, randomized starting azimuth relative to the missing wedge, and restricted angular search
Map data
Sample
  • Organelle or cellular component: Microtubule
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsCroxford M / Villa E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP2 GM123494 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Entropy-regularized deconvolution of cellular cryotransmission electron tomograms.
Authors: Matthew Croxford / Michael Elbaum / Muthuvel Arigovindan / Zvi Kam / David Agard / Elizabeth Villa / John Sedat /
Abstract: Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in ...Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).
History
DepositionJul 9, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24419.png

Downloads & links

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Map

FileDownload / File: emd_24419.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.98 Å/pix.
x 60 pix.
= 539.04 Å		8.98 Å/pix.
x 60 pix.
= 539.04 Å		8.98 Å/pix.
x 60 pix.
= 539.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.984 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-5.637181 - 7.2325454
Average (Standard dev.)-0.4315161 (±2.2809641)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 539.04004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.9848.9848.984
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z539.040539.040539.040
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-5.6377.233-0.432

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Supplemental data

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Half map: #2

Fileemd_24419_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24419_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 : Microtubule

EntireName: Microtubule
Components
  • Organelle or cellular component: Microtubule

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Supramolecule #1: Microtubule

SupramoleculeName: Microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Subtomogram average of a polymerized microtubule.
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293 / Organ: Kidney

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil / Support film - Material: CARBON
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 96.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: Dynamo (ver. 11514) / Number subtomograms used: 300
ExtractionNumber tomograms: 1 / Number images used: 300 / Method: Filament Tracing / Software - Name: Dynamo (ver. 11514)
Details: A single MT filament parallel to the tilt axis was traced and sampled every 4nm.
Final 3D classificationNumber classes: 1
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Dynamo (ver. 11514)
FSC plot (resolution estimation)

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