[English] 日本語
Yorodumi- EMDB-12699: Subtomogram average of nucleosomes extracted from cryo-tomograms ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12699 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Subtomogram average of nucleosomes extracted from cryo-tomograms of Drosophila melanogaster embryos | |||||||||||||||
Map data | Subtomogram average of nucleosomes extracted from cryo-tomograms of vitreous sections obtained from Drosophila melanogaster embryos | |||||||||||||||
Sample |
| |||||||||||||||
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 | |||||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||||||||
Method | subtomogram averaging / cryo EM | |||||||||||||||
Authors | Harastani M / Eltsov M / Leforestier A / Jonic S | |||||||||||||||
Funding support | France, Germany, 4 items
| |||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12699.map.gz | 128 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12699-v30.xml emd-12699.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_12699.png | 24.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12699 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12699 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
EM raw data | EMPIAR-10679 (Title: Subtomograms of nucleosomes extracted from cryo-tomograms of Drosophila melanogaster embryos Data size: 666.3 MB Data #1: Unaligned subtomograms of nucleosomes extracted from in situ cryo-tomograms of Drosophila melanogaster embryonic brain [subtomograms]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_12699.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Subtomogram average of nucleosomes extracted from cryo-tomograms of vitreous sections obtained from Drosophila melanogaster embryos | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : nucleosome
Entire | Name: nucleosome |
---|---|
Components |
|
-Supramolecule #1: nucleosome
Supramolecule | Name: nucleosome / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 210 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: C-flat-2/2 / Material: COPPER/PALLADIUM / Mesh: 200 / Support film - Material: CARBON |
Vitrification | Cryogen name: OTHER / Details: high pressure freezer HPM010 (ABRA Fluid AG). |
Details | Drosophila 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 3.5 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film 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 |
-Image processing
Extraction | Number tomograms: 1 / Number images used: 667 |
---|---|
Final 3D classification | Number classes: 1 / Avg.num./class: 1 |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Number subtomograms used: 600 |