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Yorodumi- EMDB-5255: Seeing the Portal in Herpes Simplex Virus type I B-capsids. Map1:... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5255 | |||||||||
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Title | Seeing the Portal in Herpes Simplex Virus type I B-capsids. Map1: Icosahedral reconstruction of the HSV-1 B-capsid Map2: symmetry free (c1) reconstruction of the HSV-1 B-capsid Map3: c12 symmetrized portal density extracted from symmetry free (c1) reconstruction of the HSV-1 B-capsid Map4: c1 portal density extracted from symmetry free (c1) reconstruction of the HSV-1 B-capsid | |||||||||
Map data | This is the non-averaged portal density extracted from the c1 (symmetry-free) reconstruction of the HSV-1 B-capsid | |||||||||
Sample |
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Keywords | Herpes / HSV1 / Portal / Cryo-EM / Single Particle / UL6 / Asymmetric / Symmetry-free | |||||||||
Biological species | Herpes Simplex Virus Type I (Herpes simplex virus type 1) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 24.0 Å | |||||||||
Authors | Rochat RH / Liu X / Murata K / Nagayama K / Rixon FJ / Chiu W | |||||||||
Citation | Journal: J Virol / Year: 2011 Title: Seeing the portal in herpes simplex virus type 1 B capsids. Authors: R H Rochat / X Liu / K Murata / K Nagayama / F J Rixon / W Chiu / Abstract: Resolving the nonicosahedral components in large icosahedral viruses remains a technical challenge in structural virology. We have used the emerging technique of Zernike phase-contrast electron ...Resolving the nonicosahedral components in large icosahedral viruses remains a technical challenge in structural virology. We have used the emerging technique of Zernike phase-contrast electron cryomicroscopy to enhance the image contrast of ice-embedded herpes simplex virus type 1 capsids. Image reconstruction enabled us to retrieve the structure of the unique portal vertex in the context of the icosahedral capsid and, for the first time, show the subunit organization of a portal in a virus infecting eukaryotes. Our map unequivocally resolves the 12-subunit portal situated beneath one of the pentameric vertices, thus removing uncertainty over the location and stoichiometry of the herpesvirus portal. | |||||||||
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_5255.map.gz | 27.7 MB | EMDB map data format | |
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Header (meta data) | emd-5255-v30.xml emd-5255.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_5255_1.png | 725.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5255 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5255 | HTTPS FTP |
-Validation report
Summary document | emd_5255_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_5255_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_5255_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5255 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5255 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5255.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the non-averaged portal density extracted from the c1 (symmetry-free) reconstruction of the HSV-1 B-capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.32 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 : Herpes simplex virus type I B-capsids
Entire | Name: Herpes simplex virus type I B-capsids |
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Components |
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-Supramolecule #1000: Herpes simplex virus type I B-capsids
Supramolecule | Name: Herpes simplex virus type I B-capsids / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1 |
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Molecular weight | Theoretical: 100 MDa |
-Supramolecule #1: Herpes Simplex Virus Type I
Supramolecule | Name: Herpes Simplex Virus Type I / type: virus / ID: 1 / Name.synonym: HSV-1 / Sci species name: Herpes Simplex Virus Type I / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HSV-1 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 200 MDa |
Virus shell | Shell ID: 1 / Name: vp5 / Diameter: 1250 Å / T number (triangulation number): 16 |
Virus shell | Shell ID: 2 / Name: vp26 / Diameter: 1250 Å / T number (triangulation number): 15 |
Virus shell | Shell ID: 3 / Name: vp19 / Diameter: 1250 Å / T number (triangulation number): 10 |
Virus shell | Shell ID: 4 / Name: vp23 / Diameter: 1250 Å / T number (triangulation number): 5 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Grid | Details: Quantifoil 2/2 grids |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 85 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification instrument: Vitrobot Mark IV / Method: Blot 1 time for 2 seconds |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 100 K / Max: 101 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Astigmatism was corrected at 400,000 times magnification |
Specialist optics | Energy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 10, 2009 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 20 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 56000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 0.2 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder: Side Entry / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were aligned using the multi-path simulated annealing algorithm. |
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CTF correction | Details: No Correction |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA Details: Reconstructions were made both with and without imposed symmetry. Number images used: 6300 |