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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5661 | |||||||||
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Title | Cryo-electron microscopy of herpesvirus simplex type 1 A-capsid | |||||||||
![]() | Reconstruction of herpesvirus simplex type 1 A-capsid | |||||||||
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![]() | herpesvirus / capsid / cryo-EM | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.9 Å | |||||||||
![]() | Homa FL / Huffman JB / Toropova K / Lopez HR / Makhov AM / Conway JF | |||||||||
![]() | ![]() Title: Structure of the pseudorabies virus capsid: comparison with herpes simplex virus type 1 and differential binding of essential minor proteins. Authors: F L Homa / J B Huffman / K Toropova / H R Lopez / A M Makhov / J F Conway / ![]() Abstract: The structure of pseudorabies virus (PRV) capsids isolated from the nucleus of infected cells and from PRV virions was determined by cryo-electron microscopy (cryo-EM) and compared to herpes simplex ...The structure of pseudorabies virus (PRV) capsids isolated from the nucleus of infected cells and from PRV virions was determined by cryo-electron microscopy (cryo-EM) and compared to herpes simplex virus type 1 (HSV-1) capsids. PRV capsid structures closely resemble those of HSV-1, including distribution of the capsid vertex specific component (CVSC) of HSV-1, which is a heterodimer of the pUL17 and pUL25 proteins. Occupancy of CVSC on all PRV capsids is near 100%, compared to ~50% reported for HSV-1 C-capsids and 25% or less that we measure for HSV-1 A- and B-capsids. A PRV mutant lacking pUL25 does not produce C-capsids and lacks visible CVSC density in the cryo-EM-based reconstruction. A reconstruction of PRV capsids in which green fluorescent protein was fused within the N-terminus of pUL25 confirmed previous studies with a similar HSV-1 capsid mutant localizing pUL25 to the CVSC density region that is distal to the penton. However, comparison of the CVSC density in a 9-Å-resolution PRV C-capsid map with the available crystal structure of HSV-1 pUL25 failed to find a satisfactory fit, suggesting either a different fold for PRV pUL25 or a capsid-bound conformation for pUL25 that does not match the X-ray model determined from protein crystallized in solution. The PRV capsid imaged within virions closely resembles C-capsids with the addition of weak but significant density shrouding the pentons that we attribute to tegument proteins. Our results demonstrate significant structure conservation between the PRV and HSV capsids. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 353.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.3 KB 9.3 KB | Display Display | ![]() |
Images | ![]() | 1.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5650C ![]() 5652C ![]() 5654C ![]() 5655C ![]() 5656C ![]() 5657C ![]() 5659C ![]() 5660C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of herpesvirus simplex type 1 A-capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Herpesvirus simplex type 1 A-capsid
Entire | Name: Herpesvirus simplex type 1 A-capsid |
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Components |
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-Supramolecule #1000: Herpesvirus simplex type 1 A-capsid
Supramolecule | Name: Herpesvirus simplex type 1 A-capsid / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Human herpesvirus 1
Supramolecule | Name: Human herpesvirus 1 / type: virus / ID: 1 / Name.synonym: HSV-1 / NCBI-ID: 10298 / Sci species name: Human herpesvirus 1 / Sci species strain: KOS / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes / Syn species name: HSV-1 |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: A-capsid / Diameter: 1250 Å / T number (triangulation number): 16 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: TNE: 500mM NaCl, 10mM Tris, 1mM EDTA |
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Grid | Details: Quantifoil R2/1, 200 mesh copper, glow discharged for 10-15 secs |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Chamber temperature: 82 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 6 seconds. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Max: 95 K |
Date | Oct 14, 2010 |
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: 48 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 29000 |
Sample stage | Specimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | Particles were picked with xdpreprocess. |
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CTF correction | Details: Each micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM(v3.13) / Number images used: 1093 |