[English] 日本語
Yorodumi- EMDB-18231: CryoDRGN Reconstruction of 80S Ribosome in Rotated State from S.c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18231 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoDRGN Reconstruction of 80S Ribosome in Rotated State from S.cerevisiae Prepared using Cryo-plasmaFIB Milling | |||||||||
Map data | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast | |||||||||
Sample |
| |||||||||
Keywords | yeast 80S / RIBOSOME | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Rangan R / Khavnekar S / Lerer A / Johnston J / Kelley R / Obr M / Kotecha A / Zhong ED | |||||||||
Funding support | Germany, 2 items
| |||||||||
Citation | Journal: Nat Methods / Year: 2024 Title: CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Authors: Ramya Rangan / Ryan Feathers / Sagar Khavnekar / Adam Lerer / Jake D Johnston / Ron Kelley / Martin Obr / Abhay Kotecha / Ellen D Zhong / Abstract: Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal ...Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal structures at molecular resolution, image processing algorithms remain a bottleneck in resolving the heterogeneity of biomolecular structures in situ. Here, we introduce cryoDRGN-ET for heterogeneous reconstruction of cryo-ET subtomograms. CryoDRGN-ET learns a deep generative model of three-dimensional density maps directly from subtomogram tilt-series images and can capture states diverse in both composition and conformation. We validate this approach by recovering the known translational states in Mycoplasma pneumoniae ribosomes in situ. We then perform cryo-ET on cryogenic focused ion beam-milled Saccharomyces cerevisiae cells. CryoDRGN-ET reveals the structural landscape of S. cerevisiae ribosomes during translation and captures continuous motions of fatty acid synthase complexes inside cells. This method is openly available in the cryoDRGN software. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_18231.map.gz | 59.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-18231-v30.xml emd-18231.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18231_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_18231.png | 81.3 KB | ||
Masks | emd_18231_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-18231.cif.gz | 4 KB | ||
Others | emd_18231_half_map_1.map.gz emd_18231_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18231 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18231 | HTTPS FTP |
-Validation report
Summary document | emd_18231_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_18231_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_18231_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_18231_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18231 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18231 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_18231.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.96 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_18231_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast
File | emd_18231_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast
File | emd_18231_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : 80S S. cerevisiae
Entire | Name: 80S S. cerevisiae |
---|---|
Components |
|
-Supramolecule #1: 80S S. cerevisiae
Supramolecule | Name: 80S S. cerevisiae / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |