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Yorodumi- EMDB-4628: Cryo-EM structure of Tobacco Mossaic Virus from microfluidic grid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4628 | |||||||||
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Title | Cryo-EM structure of Tobacco Mossaic Virus from microfluidic grid preparation. | |||||||||
Map data | ||||||||||
Sample |
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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 | helical reconstruction / cryo EM / Resolution: 1.92 Å | |||||||||
Authors | Schmidli C / Albiez S / Rima L / Righetto R / Mohammed I / Oliva P / Kovacik L / Stahlberg H / Braun T | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Microfluidic protein isolation and sample preparation for high-resolution cryo-EM. Authors: Claudio Schmidli / Stefan Albiez / Luca Rima / Ricardo Righetto / Inayatulla Mohammed / Paolo Oliva / Lubomir Kovacik / Henning Stahlberg / Thomas Braun / Abstract: High-resolution structural information is essential to understand protein function. Protein-structure determination needs a considerable amount of protein, which can be challenging to produce, often ...High-resolution structural information is essential to understand protein function. Protein-structure determination needs a considerable amount of protein, which can be challenging to produce, often involving harsh and lengthy procedures. In contrast, the several thousand to a few million protein particles required for structure determination by cryogenic electron microscopy (cryo-EM) can be provided by miniaturized systems. Here, we present a microfluidic method for the rapid isolation of a target protein and its direct preparation for cryo-EM. Less than 1 μL of cell lysate is required as starting material to solve the atomic structure of the untagged, endogenous human 20S proteasome. Our work paves the way for high-throughput structure determination of proteins from minimal amounts of cell lysate and opens more opportunities for the isolation of sensitive, endogenous protein complexes. | |||||||||
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_4628.map.gz | 33.2 MB | EMDB map data format | |
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Header (meta data) | emd-4628-v30.xml emd-4628.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4628_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_4628.png | 96.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4628 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4628 | HTTPS FTP |
-Related structure data
Related structure data | 6r7mMC 4738C 6r70C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4628.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.812 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 : Tobacco mosaic virus
Entire | Name: Tobacco mosaic virus |
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Components |
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-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: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Nicotiana tabacum (common tobacco) |
Molecular weight | Theoretical: 39.5 MDa |
Virus shell | Shell ID: 1 / Name: CP / Diameter: 180.0 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Details: CryoWriter.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 0-30 / Number grids imaged: 1 / Number real images: 523 / Average exposure time: 6.0 sec. / Average electron dose: 72.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |