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Open data
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Basic information
Entry | Database: PDB / ID: 6r7m | |||||||||
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Title | Tobacco Mosaic Virus (TMV) | |||||||||
![]() | Capsid protein![]() | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() helical viral capsid / structural molecule activity / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Schmidli, C. / Albiez, S. / Rima, L. / Righetto, R. / Mohammed, I. / Oliva, P. / Kovacik, L. / Stahlberg, H. / Braun, T. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.9 KB | Display | ![]() |
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PDB format | ![]() | 25.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4628MC ![]() 4738C ![]() 6r70C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 40 / Rise per n subunits: 1.41 Å / Rotation per n subunits: 22.03 °) |
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Components
#1: Protein | ![]() Mass: 17091.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Tobacco mosaic virus![]() |
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Molecular weight | Value: 39.5 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Nicotiana tabacum |
Virus shell | Name: CP / Diameter: 180 nm |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification![]() | Cryogen name: ETHANE / Details: CryoWriter |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6 sec. / Electron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 523 |
Image scans | Width: 7676 / Height: 7420 / Movie frames/image: 30 / Used frames/image: 0-30 |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 22.03 ° / Axial rise/subunit: 1.41 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2676 | |||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52776 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6I5A Accession code: 6I5A / Source name: PDB / Type: experimental model |