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- EMDB-1905: Residues of the UL25 Protein of Herpes Simplex Virus That Are Req... -

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Basic information

Entry
Database: EMDB / ID: EMD-1905
TitleResidues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids.
Map dataSurface 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
  • Sample: HSV-1 C-capsid with the UL25 protein labeled with a tandem affinity purification (TAP) tag at amino acid 50.
  • Virus: Human herpesvirus 1 strain KOS
KeywordsHSV-1 / UL25 / CVSC / cryo-EM
Biological speciesHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 14.7 Å
AuthorsCockrell SK / Huffman JB / Toropova K / Conway JF / Homa FL
CitationJournal: 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
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: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1905.png

Downloads & links

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Map

FileDownload / File: emd_1905.map.gz / Format: CCP4 / Size: 111 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface 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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 310 pix.
= 787.4 Å		2.54 Å/pix.
x 310 pix.
= 787.4 Å		2.54 Å/pix.
x 310 pix.
= 787.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.2.542.542.54
CCP4 map header2.542.542.54
EM Navigator Movie #15.085.085.08
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-7.12019396 - 6.77211857
Average (Standard dev.)0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 787.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z310310310
origin x/y/z0.0000.0000.000
length x/y/z787.400787.400787.400
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/NS310310310
D min/max/mean-7.1206.7720.000

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Supplemental data

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Sample components

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Entire : HSV-1 C-capsid with the UL25 protein labeled with a tandem affini...

EntireName: HSV-1 C-capsid with the UL25 protein labeled with a tandem affinity purification (TAP) tag at amino acid 50.
Components
  • Sample: HSV-1 C-capsid with the UL25 protein labeled with a tandem affinity purification (TAP) tag at amino acid 50.
  • Virus: Human herpesvirus 1 strain KOS

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Supramolecule #1000: HSV-1 C-capsid with the UL25 protein labeled with a tandem affini...

SupramoleculeName: 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

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: ETHANE / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot mark III / Method: 6s blot prior to plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
DateOct 9, 2009
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: 83 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.73 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 50000
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: 14.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 4865

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