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- EMDB-1903: The HSV-1 UL17 protein is the second constituent of the capsid ve... -

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Basic information

Entry
Database: EMDB / ID: EMD-1903
TitleThe HSV-1 UL17 protein is the second constituent of the capsid vertex specific component (CVSC) required for DNA packaging and retention.
Map dataSurface rendered view of a HSV-1 C-capsid where protein UL17 has been genetically tagged with GFP at its C-terminus
Sample
  • Sample: HSV-1 C-capsid with UL17 protein labeled with GFP at its C terminus.
  • Virus: Human herpesvirus 1 strain KOS
KeywordsHSV-1 / UL17 / UL25 / CVSC / cryo-EM / virus structure
Biological speciesHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsToropova K / Huffman JB / Homa FL / Conway JF
CitationJournal: 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
DepositionJun 7, 2011-
Header (metadata) releaseOct 3, 2012-
Map releaseOct 3, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1903.png

Downloads & links

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Map

FileDownload / File: emd_1903.map.gz / Format: CCP4 / Size: 985.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendered view of a HSV-1 C-capsid where protein UL17 has been genetically tagged with GFP at its C-terminus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.12 Å/pix.
x 642 pix.
= 1361.04 Å		2.12 Å/pix.
x 642 pix.
= 1361.04 Å		2.12 Å/pix.
x 642 pix.
= 1361.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-6.45088243 - 5.97226095
Average (Standard dev.)-0.00000002 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions642642642
Spacing642642642
CellA=B=C: 1361.0399 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.122.122.12
M x/y/z642642642
origin x/y/z0.0000.0000.000
length x/y/z1361.0401361.0401361.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS642642642
D min/max/mean-6.4515.972-0.000

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Supplemental data

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Sample components

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Entire : HSV-1 C-capsid with UL17 protein labeled with GFP at its C terminus.

EntireName: HSV-1 C-capsid with UL17 protein labeled with GFP at its C terminus.
Components
  • Sample: HSV-1 C-capsid with UL17 protein labeled with GFP at its C terminus.
  • Virus: Human herpesvirus 1 strain KOS

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Supramolecule #1000: HSV-1 C-capsid with UL17 protein labeled with GFP at its C terminus.

SupramoleculeName: HSV-1 C-capsid with UL17 protein labeled with GFP at its C terminus.
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 1 strain KOS

SupramoleculeName: 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 shellShell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 500 mM NaCl, 10 mM Tris, 1 mM EDTA
VitrificationCryogen name: OTHER / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK III
Details: Vitrification instrument: Vitrobot mark III. Cryogen was an equal mix of ethane - propane
Method: 7 second blot before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
DateSep 3, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 134 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.06 µm / Nominal defocus min: 1.65 µm / Nominal magnification: 29000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flip each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 3984

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