+Open data
-Basic information
Entry | Database: PDB / ID: 7txj | |||||||||
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Title | Cryo-EM of AFV6 | |||||||||
Components |
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Keywords | VIRUS / helical symmetry / archaeal virus | |||||||||
Function / homology | DNA / DNA (> 10) / Structural protein / Structural protein Function and homology information | |||||||||
Biological species | Acidianus filamentous virus 6 | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wang, F. / Cvirkaite-Krupovic, V. / Krupovic, M. / Egelman, E.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Cryo-EM of AFV6 Authors: Wang, F. / Cvirkaite-Krupovic, V. / Krupovic, M. / Egelman, E.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7txj.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7txj.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 7txj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7txj_validation.pdf.gz | 783.8 KB | Display | wwPDB validaton report |
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Full document | 7txj_full_validation.pdf.gz | 783.4 KB | Display | |
Data in XML | 7txj_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 7txj_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7txj ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txj | HTTPS FTP |
-Related structure data
Related structure data | 26159MC 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 |
EM raw data | EMPIAR-11040 (Title: Micrographs of viruses ATV and AFV6 / Data size: 218.0 Data #1: raw micrographs and gain reference [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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3 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 5.75 Å / Rotation per n subunits: 38.461 °) |
-Components
#1: DNA chain | Mass: 3659.440 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acidianus filamentous virus 6 #2: Protein | | Mass: 18593.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acidianus filamentous virus 6 / References: UniProt: A7WKI9 #3: Protein | | Mass: 22751.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acidianus filamentous virus 6 / References: UniProt: A7WKJ0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Acidianus filamentous virus 6 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Acidianus filamentous virus 6 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 38.46 ° / Axial rise/subunit: 5.75 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78141 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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