+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8252 | |||||||||
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Title | 2.6A 3D reconstruction of Tulane virus | |||||||||
Map data | reconstruction of Tulane virus | |||||||||
Sample |
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Biological species | Tulane virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Yu G / Li K / Jiang W | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Antibody-Based Affinity Cryoelectron Microscopy at 2.6-Å Resolution. Authors: Guimei Yu / Kunpeng Li / Pengwei Huang / Xi Jiang / Wen Jiang / Abstract: The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging ...The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8252.map.gz | 210.2 MB | EMDB map data format | |
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Header (meta data) | emd-8252-v30.xml emd-8252.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8252_fsc.xml | 26.2 KB | Display | FSC data file |
Images | emd_8252.png | 181.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8252 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8252 | HTTPS FTP |
-Validation report
Summary document | emd_8252_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_8252_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_8252_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8252 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8252 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8252.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of Tulane virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.975 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tulane virus
Entire | Name: Tulane virus |
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Components |
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-Supramolecule #1: Tulane virus
Supramolecule | Name: Tulane virus / type: virus / ID: 1 / Parent: 0 / Details: Purified from cell cultures / NCBI-ID: 512169 / Sci species name: Tulane virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Host system | Organism: Platyrrhini (New World monkeys) / Recombinant cell: Monkey kidney cells / Recombinant plasmid: pBR322 |
Molecular weight | Theoretical: 10 MDa |
Virus shell | Shell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 1x PBS |
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Grid | Model: Ted Pella ultrathin carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-25 / Number grids imaged: 1 / Number real images: 1000 / Average electron dose: 5.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |