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- EMDB-22595: HVS-1 ul17null B-caspid, C5 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-22595
TitleHVS-1 ul17null B-caspid, C5 symmetry
Map dataUL17null B-caspid C5 sym
Sample
  • Virus: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsHuet A / Huffman JB / Conway JF / Homa FL
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)AI089803 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)S10 OD019995 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)AI132967 United States
CitationJournal: J Virol / Year: 2020
Title: Role of the Herpes Simplex Virus CVSC Proteins at the Capsid Portal Vertex.
Authors: Alexis Huet / Jamie B Huffman / James F Conway / Fred L Homa /
Abstract: The packaging of DNA into preformed capsids is a critical step during herpesvirus infection. For herpes simplex virus, this process requires the products of seven viral genes: the terminase proteins ...The packaging of DNA into preformed capsids is a critical step during herpesvirus infection. For herpes simplex virus, this process requires the products of seven viral genes: the terminase proteins pUL15, pUL28, and pUL33; the capsid vertex-specific component (CVSC) proteins pUL17 and pUL25; and the portal proteins pUL6 and pUL32. The pUL6 portal dodecamer is anchored at one vertex of the capsid by interactions with the adjacent triplexes as well as helical density attributed to the pUL17 and pUL25 subunits of the CVSC. To define the roles and structures of the CVSC proteins in virus assembly and DNA packaging, we isolated a number of recombinant viruses expressing pUL25, pUL17, and pUL36 fused with green or red fluorescent proteins as well as viruses with specific deletions in the CVSC genes. Biochemical and structural studies of these mutants demonstrated that (i) four of the helices in the CVSC helix bundle can be attributed to two copies each of pUL36 and pUL25, (ii) pUL17 and pUL6 are required for capsid binding of the terminase complex in the nucleus, (iii) pUL17 is important for determining the site of the first cleavage reaction generating replicated genomes with termini derived from the long-arm component of the herpes simplex virus 1 (HSV-1) genome, (iv) pUL36 serves no direct role in cleavage/packaging, (v) cleavage and stable packaging of the viral genome involve an ordered interaction of the terminase complex and pUL25 with pUL17 at the portal vertex, and (vi) packaging of the viral genome results in a dramatic displacement of the portal. Herpes simplex virus 1 (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. A critical step during productive HSV-1 infection is the cleavage and packaging of replicated, concatemeric viral DNA into preformed capsids. A key knowledge gap is how the capsid engages the replicated viral genome and the subsequent packaging of a unit-length HSV genome. Here, biochemical and structural studies focused on the unique portal vertex of wild-type HSV and packaging mutants provide insights into the mechanism of HSV genome packaging. The significance of our research is in identifying the portal proteins pUL6 and pUL17 as key viral factors for engaging the terminase complex with the capsid and the subsequent cleavage, packaging, and stable incorporation of the viral genome in the HSV-1 capsid.
History
DepositionSep 4, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22595.png

Downloads & links

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Map

FileDownload / File: emd_22595.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUL17null B-caspid C5 sym
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 600 pix.
= 1380. Å		2.3 Å/pix.
x 600 pix.
= 1380. Å		2.3 Å/pix.
x 600 pix.
= 1380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.06494506 - 0.09995781
Average (Standard dev.)0.0030597225 (±0.010428445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 1380.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z1380.0001380.0001380.000
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0650.1000.003

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Supplemental data

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Sample components

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Entire : Human alphaherpesvirus 1

EntireName: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Components
  • Virus: Human alphaherpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1: Human alphaherpesvirus 1

SupramoleculeName: Human alphaherpesvirus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10298 / Sci species name: Human alphaherpesvirus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Chlorocebus sabaeus (green monkey) / Recombinant cell: vero / Recombinant plasmid: BAC
Molecular weightTheoretical: 145 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 1250.0 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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
10.0 mMTris
500.0 mMsodium chlorideNaCl
1.0 mMEDTA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II / Details: 8 sec blot.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3000 / Average exposure time: 1.65 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 93000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1785
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1785
Initial angle assignmentType: COMMON LINE / Software - Name: RELION
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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