[English] 日本語
Yorodumi- EMDB-10834: Tobacco mosaic virus (TMV) structure determined by a hybrid STA-S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10834 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tobacco mosaic virus (TMV) structure determined by a hybrid STA-SPA workflow | |||||||||
Map data | refine map | |||||||||
Sample |
| |||||||||
Function / homology | Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein / Capsid protein Function and homology information | |||||||||
Biological species | Tobacco mosaic virus | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 5.24 Å | |||||||||
Authors | Sanchez RM / Zhang Y / Chen W / Dietrich L / Kudryashev M | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM. Authors: Ricardo M Sanchez / Yingyi Zhang / Wenbo Chen / Lea Dietrich / Mikhail Kudryashev / Abstract: Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace ...Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace due to beam-induced sample drift, images with poor signal-to-noise ratios (SNR), challenges in CTF correction, and limited particle number. Here we address these issues by collecting tilt series with a higher electron dose at the zero-degree tilt. Particles of interest are then located within reconstructed tomograms, processed by conventional StA, and then re-extracted from the high-dose images in 2D. Single particle analysis tools are then applied to refine the 2D particle alignment and generate a reconstruction. Use of our hybrid StA (hStA) workflow improved the resolution for tobacco mosaic virus from 7.2 to 4.4 Å and for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. These resolution gains make hStA a promising approach for other StA projects aimed at achieving subnanometer resolution. #2: Journal: Biorxiv / Year: 2020 Title: Subnanometer-resolution structure determination in situ by a hybrid subtomogram averaging - single particle cryoEM - workflow Authors: Sanchez RM / Zhang Y / Chen W / Dietrich L / Kudryashev M | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10834.map.gz | 22.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10834-v30.xml emd-10834.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10834_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_10834.png | 35.3 KB | ||
Masks | emd_10834_msk_1.map | 30.5 MB | Mask map | |
Others | emd_10834_half_map_1.map.gz emd_10834_half_map_2.map.gz | 23.1 MB 23.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10834 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10834 | HTTPS FTP |
-Validation report
Summary document | emd_10834_validation.pdf.gz | 522.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_10834_full_validation.pdf.gz | 521.5 KB | Display | |
Data in XML | emd_10834_validation.xml.gz | 12.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10834 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10834 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10393 (Title: Subnanometer-resolution structure determination in situ by a hybrid subtomogram averaging - single particle cryoEM - workflow - on TMV Data size: 37.5 Data #1: TMV-hybrid tomography- tiltstacks- aligned and CTF corrected [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_10834.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | refine map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_10834_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_10834_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_10834_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Tobacco mosaic virus
Entire | Name: Tobacco mosaic virus |
---|---|
Components |
|
-Supramolecule #1: Tobacco mosaic virus
Supramolecule | Name: Tobacco mosaic virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Virus shell | Shell ID: 1 / Name: Capsid protein / Diameter: 180.0 Å |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | helical array |
-Sample preparation
Concentration | 33 mg/mL |
---|---|
Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.0045 µm / Nominal defocus min: -0.0035 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |