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- EMDB-10195: Doublecortin N-terminal DC-domain (NDC)-decorated 13-protofilamen... -

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Basic information

Entry
Database: EMDB / ID: EMD-10195
TitleDoublecortin N-terminal DC-domain (NDC)-decorated 13-protofilament microtubule (GDP state) processed with MiRP (Microtubule Relion-based Pipeline)
Map dataC1 reconstruction of 13-protofilament GDP-microtubule decorated with NDC-NDC chimera of human doublecortin
Sample
  • Complex: 13-protofilament microtubule decorated with NDC-NDC chimera of human doublecortin
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCook AC / Manka SW / Wang S / Moores CA / Atherton J
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/R000352/1 United Kingdom
Wellcome Trust079605/Z/06/Z United Kingdom
Medical Research Council (United Kingdom)MR/J003867/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L014211/1 United Kingdom
Wellcome Trust101488/Z/13/Z United Kingdom
CitationJournal: J Struct Biol / Year: 2020
Title: A microtubule RELION-based pipeline for cryo-EM image processing.
Authors: Alexander D Cook / Szymon W Manka / Su Wang / Carolyn A Moores / Joseph Atherton /
Abstract: Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall ...Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.
History
DepositionAug 6, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10195.png

Downloads & links

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Map

FileDownload / File: emd_10195.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1 reconstruction of 13-protofilament GDP-microtubule decorated with NDC-NDC chimera of human doublecortin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 432 pix.
= 600.48 Å		1.39 Å/pix.
x 432 pix.
= 600.48 Å		1.39 Å/pix.
x 432 pix.
= 600.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.016921937 - 0.04477428
Average (Standard dev.)0.0004743474 (±0.003701535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 600.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z600.480600.480600.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0170.0450.000

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Supplemental data

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Additional map: None

Fileemd_10195_additional.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: None

Fileemd_10195_additional_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 13-protofilament microtubule decorated with NDC-NDC chimera of hu...

EntireName: 13-protofilament microtubule decorated with NDC-NDC chimera of human doublecortin
Components
  • Complex: 13-protofilament microtubule decorated with NDC-NDC chimera of human doublecortin

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Supramolecule #1: 13-protofilament microtubule decorated with NDC-NDC chimera of hu...

SupramoleculeName: 13-protofilament microtubule decorated with NDC-NDC chimera of human doublecortin
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsMicrotubule RELION-based pipeline (MiRP)
Final reconstructionApplied symmetry - Helical parameters - Δz: 9.46 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.67 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33392
Final angle assignmentType: NOT APPLICABLE

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