Journal: J Virol / Year: 2011 Title: The herpes simplex virus 1 UL17 protein is the second constituent of the capsid vertex-specific component required for DNA packaging and retention. Authors: Katerina Toropova / Jamie B Huffman / Fred L Homa / James F Conway / Abstract: The herpes simplex virus (HSV) UL17 and UL25 minor capsid proteins are essential for DNA packaging. They are thought to comprise a molecule arrayed in five copies around each of the capsid vertices. ...The herpes simplex virus (HSV) UL17 and UL25 minor capsid proteins are essential for DNA packaging. They are thought to comprise a molecule arrayed in five copies around each of the capsid vertices. This molecule was initially termed the "C-capsid-specific component" (CCSC) (B. L. Trus et al., Mol. Cell 26:479-489, 2007), but as we have subsequently observed this feature on reconstructions of A, B, and C capsids, we now refer to it more generally as the "capsid vertex-specific component" (CVSC) (S. K. Cockrell et al., J. Virol. 85:4875-4887, 2011). We previously confirmed that UL25 occupies the vertex-distal region of the CVSC density by visualizing a large UL25-specific tag in reconstructions calculated from cryo-electron microscopy (cryo-EM) images. We have pursued the same strategy to determine the capsid location of the UL17 protein. Recombinant viruses were generated that contained either a small tandem affinity purification (TAP) tag or the green fluorescent protein (GFP) attached to the C terminus of UL17. Purification of the TAP-tagged UL17 or a similarly TAP-tagged UL25 protein clearly demonstrated that the two proteins interact. A cryo-EM reconstruction of capsids containing the UL17-GFP protein reveals that UL17 is the second component of the CVSC and suggests that UL17 interfaces with the other CVSC component, UL25, through its C terminus. The portion of UL17 nearest the vertex appears to be poorly constrained, which may provide flexibility in interacting with tegument proteins or the DNA-packaging machinery at the portal vertex. The exposed locations of the UL17 and UL25 proteins on the HSV-1 capsid exterior suggest that they may be attractive targets for highly specific antivirals.
History
Deposition
Jun 7, 2011
-
Header (metadata) release
Oct 3, 2012
-
Map release
Oct 3, 2012
-
Update
Oct 10, 2012
-
Current status
Oct 10, 2012
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_1902.map.gz / Format: CCP4 / Size: 985.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Surface rendered view of HSV-1 C-capsid
Voxel size
X=Y=Z: 2.12 Å
Density
Contour Level
By AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum
-6.3683939 - 6.07280588
Average (Standard dev.)
0.0 (±1.0)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
642
642
642
Spacing
642
642
642
Cell
A=B=C: 1361.0399 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.12
2.12
2.12
M x/y/z
642
642
642
origin x/y/z
0.000
0.000
0.000
length x/y/z
1361.040
1361.040
1361.040
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-56
-56
-55
NX/NY/NZ
112
112
112
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
642
642
642
D min/max/mean
-6.368
6.073
0.000
-
Supplemental data
-
Sample components
-
Entire : HSV-1 wild type C-capsid (KOS).
Entire
Name: HSV-1 wild type C-capsid (KOS).
Components
Sample: HSV-1 wild type C-capsid (KOS).
Virus: Human herpesvirus 1 strain KOS
-
Supramolecule #1000: HSV-1 wild type C-capsid (KOS).
Supramolecule
Name: HSV-1 wild type C-capsid (KOS). / type: sample / ID: 1000 / Number unique components: 1
-
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
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
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Buffer
pH: 7.5 / Details: 500 mM NaCl, 10 mM Tris, 1 mM EDTA
Vitrification
Cryogen name: ETHANE / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot mark III / Method: 7.5 second blot before plunging
-
Electron microscopy
Microscope
FEI TECNAI F20
Date
Jul 7, 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: FIELD EMISSION GUN
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi