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Yorodumi- EMDB-10238: Focused Classification of the vertex region of Bacteriophage PR77... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10238 | ||||||||||||
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Title | Focused Classification of the vertex region of Bacteriophage PR772 showing the heteropentameric penton | ||||||||||||
Map data | Focused Classification of the vertex region of Bacteriophage PR772 showing the heteropentameric penton | ||||||||||||
Sample |
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Biological species | Enterobacteria phage PR772 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.25 Å | ||||||||||||
Authors | Narayana Reddy HK / Svenda M | ||||||||||||
Funding support | Sweden, 3 items
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Citation | Journal: Elife / Year: 2019 Title: Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture. Authors: Hemanth Kn Reddy / Marta Carroni / Janos Hajdu / Martin Svenda / Abstract: Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged ...Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection. | ||||||||||||
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_10238.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-10238-v30.xml emd-10238.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_10238.png | 263.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10238 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10238 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10238.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Focused Classification of the vertex region of Bacteriophage PR772 showing the heteropentameric penton | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 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 : Bacteriophage PR772
Entire | Name: Bacteriophage PR772 |
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Components |
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-Supramolecule #1: Bacteriophage PR772
Supramolecule | Name: Bacteriophage PR772 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: Wild type |
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Source (natural) | Organism: Enterobacteria phage PR772 (virus) |
Molecular weight | Theoretical: 100 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 3-40 / Number grids imaged: 1 / Number real images: 3200 / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 56000 |
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CTF correction | Software - Name: RELION (ver. 3.0.7) |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7) |
Final 3D classification | Software - Name: RELION (ver. 3.0.7) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.0.7) / Number images used: 2784480 |
-Atomic model buiding 1
Software | Name: Coot (ver. 0.8.9.1) |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 104.93 / Target criteria: Cross-correlation coefficient |