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- EMDB-12699: Subtomogram average of nucleosomes extracted from cryo-tomograms ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12699
TitleSubtomogram average of nucleosomes extracted from cryo-tomograms of Drosophila melanogaster embryos
Map dataSubtomogram average of nucleosomes extracted from cryo-tomograms of vitreous sections obtained from Drosophila melanogaster embryos
Sample
  • Complex: nucleosome
Function / homology
Function and homology information


pericentric heterochromatin => GO:0005721 / condensed chromosome, centromeric region => GO:0000779 / kinetochore => GO:0000776 / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones ...pericentric heterochromatin => GO:0005721 / condensed chromosome, centromeric region => GO:0000779 / kinetochore => GO:0000776 / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / spindle attachment to meiosis I kinetochore / polytene chromosome / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / nucleosomal DNA binding / nuclear chromosome / pericentric heterochromatin / chromosome segregation / kinetochore / nucleosome assembly / structural constituent of chromatin / nucleosome / mitotic cell cycle / chromosome / chromatin organization / nucleic acid binding / protein heterodimerization activity / chromatin / protein-containing complex binding / DNA binding / identical protein binding / nucleus
Similarity search - Function
CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / Histone H2B signature. / Histone H2B ...CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / RmlC-like jelly roll fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B / Histone H3 / Histone H4 / Histone H2A / CENP-C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM
AuthorsHarastani M / Eltsov M / Leforestier A / Jonic S
Funding support France, Germany, 4 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-01 France
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-03 France
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0008-01 France
German Research Foundation (DFG)EL 861/1 Germany
CitationJournal: Front Mol Biosci / Year: 2021
Title: HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes.
Authors: Mohamad Harastani / Mikhail Eltsov / Amélie Leforestier / Slavica Jonic /
Abstract: Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (). Its potential of providing information on the dynamics of macromolecular ...Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (). Its potential of providing information on the dynamics of macromolecular complexes in cells is still largely unexploited, due to the challenges of the data analysis. The crowded cell environment and continuous conformational changes of complexes make difficult disentangling the data heterogeneity. We present HEMNMA-3D, which is, to the best of our knowledge, the first method for analyzing cryo electron subtomograms in terms of continuous conformational changes of complexes. HEMNMA-3D uses a combination of elastic and rigid-body 3D-to-3D iterative alignments of a flexible 3D reference (atomic structure or electron microscopy density map) to match the conformation, orientation, and position of the complex in each subtomogram. The elastic matching combines molecular mechanics simulation (Normal Mode Analysis of the 3D reference) and experimental, subtomogram data analysis. The rigid-body alignment includes compensation for the missing wedge, due to the limited tilt angle of cryo-ET. The conformational parameters (amplitudes of normal modes) of the complexes in subtomograms obtained through the alignment are processed to visualize the distribution of conformations in a space of lower dimension (typically, 2D or 3D) referred to as space of conformations. This allows a visually interpretable insight into the dynamics of the complexes, by calculating 3D averages of subtomograms with similar conformations from selected (densest) regions and by recording movies of the 3D reference's displacement along selected trajectories through the densest regions. We describe HEMNMA-3D and show its validation using synthetic datasets. We apply HEMNMA-3D to an experimental dataset describing nucleosome conformational variability. HEMNMA-3D software is available freely (open-source) as part of ContinuousFlex plugin of Scipion V3.0 (http://scipion.i2pc.es).
History
DepositionMar 31, 2021-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12699.png

Downloads & links

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Map

FileDownload / File: emd_12699.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of nucleosomes extracted from cryo-tomograms of vitreous sections obtained from Drosophila melanogaster embryos
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.4 Å/pix.
x 64 pix.
= 281.6 Å		4.4 Å/pix.
x 64 pix.
= 281.6 Å		4.4 Å/pix.
x 64 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.07 / Movie #1: 1.07
Minimum - Maximum-1.8754987 - 2.7774312
Average (Standard dev.)0.0044978904 (±0.21715187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.44.44.4
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-1.8752.7770.004

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Supplemental data

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Sample components

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Entire : nucleosome

EntireName: nucleosome
Components
  • Complex: nucleosome

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Supramolecule #1: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 210 KDa

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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: 7.5
GridModel: C-flat-2/2 / Material: COPPER/PALLADIUM / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: OTHER / Details: high pressure freezer HPM010 (ABRA Fluid AG).
DetailsDrosophila melanogaster embryos were high-pressure frozen. Vitreous sections were cut with a nominal thickness of 75 nm and collected onto 200 mesh C-flat grids

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 3.5 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 1 / Number images used: 667
Final 3D classificationNumber classes: 1 / Avg.num./class: 1
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Number subtomograms used: 600

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