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Yorodumi- PDB-5lqp: Cryo-EM reconstruction of bacteriophage AP205 virus-like particles. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lqp | ||||||
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Title | Cryo-EM reconstruction of bacteriophage AP205 virus-like particles. | ||||||
Components | Coat protein | ||||||
Keywords | VIRUS LIKE PARTICLE / RNA bacteriophage / Leviviridae / coat protein / virus-like particle | ||||||
Function / homology | viral capsid / Coat protein Function and homology information | ||||||
Biological species | Acinetobacter phage AP205 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å | ||||||
Authors | Diebolder, C.A. / Rumnieks, J. / Tars, K. / Koning, R.I. | ||||||
Citation | Journal: J Mol Biol / Year: 2016 Title: Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages. Authors: Mihails Shishovs / Janis Rumnieks / Christoph Diebolder / Kristaps Jaudzems / Loren B Andreas / Jan Stanek / Andris Kazaks / Svetlana Kotelovica / Inara Akopjana / Guido Pintacuda / Roman I ...Authors: Mihails Shishovs / Janis Rumnieks / Christoph Diebolder / Kristaps Jaudzems / Loren B Andreas / Jan Stanek / Andris Kazaks / Svetlana Kotelovica / Inara Akopjana / Guido Pintacuda / Roman I Koning / Kaspars Tars / Abstract: AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus- ...AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5lqp.cif.gz | 3.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5lqp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5lqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lqp ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lqp | HTTPS FTP |
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-Related structure data
Related structure data | 4098MC 5fs4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 13820.569 Da / Num. of mol.: 180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter phage AP205 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AZ42 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: AP205 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Acinetobacter phage AP205 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K |
-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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 8 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
EM imaging optics | Energyfilter name: FEI SFEG |
Image scans | Movie frames/image: 7 / Used frames/image: 1-7 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 63253 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2215 / Symmetry type: POINT |