+Open data
-Basic information
Entry | Database: PDB / ID: 7q23 | ||||||
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Title | cryo iDPC-STEM structure recorded with CSA 3.0 | ||||||
Components |
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Keywords | VIRUS / tobacco mosaic virus / RNA virus | ||||||
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 / RNA / Capsid protein Function and homology information | ||||||
Biological species | Tobacco mosaic virus | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Sachse, C. / Leidl, M.L. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Methods / Year: 2022 Title: Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution. Authors: Ivan Lazić / Maarten Wirix / Max Leo Leidl / Felix de Haas / Daniel Mann / Maximilian Beckers / Evgeniya V Pechnikova / Knut Müller-Caspary / Ricardo Egoavil / Eric G T Bosch / Carsten Sachse / Abstract: In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently ...In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC-STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC-STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q23.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q23.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 7q23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q23_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7q23_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7q23_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 7q23_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/7q23 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q23 | HTTPS FTP |
-Related structure data
Related structure data | 13779MC 7q22C 7q2qC 7q2rC 7q2sC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 17091.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tobacco mosaic virus (strain vulgare) / Strain: vulgare / References: UniProt: P69687 |
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#2: RNA chain | Mass: 958.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tobacco mosaic virus (strain vulgare) / Strain: vulgare |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Tobacco mosaic virus / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 131 kDa/nm |
Source (natural) | Organism: Tobacco mosaic virus (strain vulgare) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 90 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: blot force of +10 and a duration for blotting of 10 seconds |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: iDPC-STEM |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: OTHER |
-Processing
EM software |
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Image processing | Details: iDPC-STEM | ||||||||||||
CTF correction | Type: NONE | ||||||||||||
Helical symmerty | Angular rotation/subunit: 22.03 ° / Axial rise/subunit: 1.408 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1392 / Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||
Atomic model building | PDB-ID: 4UDV Accession code: 4UDV / Source name: PDB / Type: experimental model |