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Yorodumi- EMDB-1905: Residues of the UL25 Protein of Herpes Simplex Virus That Are Req... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1905 | |||||||||
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Title | Residues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids. | |||||||||
Map data | Surface view of HSV-1 C-capsid where the UL25 protein has been genetically tagged with a tandem affinity purification (TAP) tag at its N-terminus. | |||||||||
Sample |
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Keywords | HSV-1 / UL25 / CVSC / cryo-EM | |||||||||
Biological species | Human herpesvirus 1 strain KOS | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.7 Å | |||||||||
Authors | Cockrell SK / Huffman JB / Toropova K / Conway JF / Homa FL | |||||||||
Citation | Journal: J Virol / Year: 2011 Title: Residues of the UL25 protein of herpes simplex virus that are required for its stable interaction with capsids. Authors: Shelley K Cockrell / Jamie B Huffman / Katerina Toropova / James F Conway / Fred L Homa / Abstract: The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface ...The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated recombinant viruses with either small truncations or amino acid substitutions in the UL25 N terminus. Studies of these mutants demonstrated that there are two important regions within the capsid binding domain. The first 27 amino acids are essential for capsid binding of UL25, while residues 26 to 39, which are highly conserved in the UL25 homologues of other alphaherpesviruses, were found to be critical for stable capsid binding. Cryo-electron microscopy reconstructions of capsids containing either a small tag on the N terminus of UL25 or the green fluorescent protein (GFP) fused between amino acids 50 and 51 of UL25 demonstrate that residues 1 to 27 of UL25 contact the hexon adjacent to the penton. A second region, most likely centered on amino acids 26 to 39, contacts the triplex that is one removed from the penton. Importantly, both of these UL25 capsid binding regions are essential for the stable packaging of full-length viral genomes. | |||||||||
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_1905.map.gz | 54.3 MB | EMDB map data format | |
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Header (meta data) | emd-1905-v30.xml emd-1905.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | EMD-1905.png | 198.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1905 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1905.map.gz / Format: CCP4 / Size: 111 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface view of HSV-1 C-capsid where the UL25 protein has been genetically tagged with a tandem affinity purification (TAP) tag at its N-terminus. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HSV-1 C-capsid with the UL25 protein labeled with a tandem affini...
Entire | Name: HSV-1 C-capsid with the UL25 protein labeled with a tandem affinity purification (TAP) tag at amino acid 50. |
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Components |
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-Supramolecule #1000: HSV-1 C-capsid with the UL25 protein labeled with a tandem affini...
Supramolecule | Name: HSV-1 C-capsid with the UL25 protein labeled with a tandem affinity purification (TAP) tag at amino acid 50. type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Human herpesvirus 1 strain KOS
Supramolecule | Name: Human herpesvirus 1 strain KOS / type: virus / ID: 1 / Name.synonym: HSV-1 / NCBI-ID: 10306 / Sci species name: Human herpesvirus 1 strain KOS / Virus type: VIRION / 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 |
Virus shell | Shell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 500 mM NaCl, 10 mM Tris, 1 mM EDTA |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot mark III / Method: 6s blot prior to plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.73 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Date | Oct 9, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 83 / Bits/pixel: 8 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Phase flip each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 4865 |