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- EMDB-5660: Cryo-electron microscopy of herpesvirus simplex type 1 B-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5660
TitleCryo-electron microscopy of herpesvirus simplex type 1 B-capsid
Map dataReconstruction of herpes simplex virus type 1 B-capsid
Sample
  • Sample: herpesvirus simplex type 1 B-capsid
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)
Keywordsherpesvirus / capsid / cryo-EM
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.9 Å
AuthorsHoma FL / Huffman JB / Toropova K / Lopez HR / Makhov AM / Conway JF
CitationJournal: J Mol Biol / Year: 2013
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
DepositionMay 2, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 10, 2013-
UpdateSep 4, 2013-
Current statusSep 4, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5660.tif

Downloads & links

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Map

FileDownload / File: emd_5660.map.gz / Format: CCP4 / Size: 704 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of herpes simplex virus type 1 B-capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.12 Å/pix.
x 723 pix.
= 1532.76 Å		2.12 Å/pix.
x 723 pix.
= 1532.76 Å		2.12 Å/pix.
x 723 pix.
= 1532.76 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: 3000.0 / Movie #1: 3000
Minimum - Maximum-22891.0 - 32443.0
Average (Standard dev.)1882.478515629999947 (±5712.478515630000402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions723723723
Spacing723723723
CellA=B=C: 1532.7599 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.122.122.12
M x/y/z723723723
origin x/y/z0.0000.0000.000
length x/y/z1532.7601532.7601532.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS723723723
D min/max/mean-22891.00032443.0001882.479

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Supplemental data

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Sample components

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Entire : herpesvirus simplex type 1 B-capsid

EntireName: herpesvirus simplex type 1 B-capsid
Components
  • Sample: herpesvirus simplex type 1 B-capsid
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1000: herpesvirus simplex type 1 B-capsid

SupramoleculeName: herpesvirus simplex type 1 B-capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 1

SupramoleculeName: Human herpesvirus 1 / type: virus / ID: 1 / Name.synonym: HSV-1 / Details: B-capsid retains remnants of proteolysed scaffold. / 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
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: B-capsid / 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: TNE: 500mM NaCl, 10mM Tris, 1mM EDTA
GridDetails: Quantifoil R2/1, 200 mesh copper, glow discharged for 10-15 secs
VitrificationCryogen 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

MicroscopeFEI TECNAI F20
TemperatureMax: 95 K
DateOct 14, 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: 48 / 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 mm / Nominal magnification: 29000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were picked with xdpreprocess.
CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM(v3.13) / Number images used: 1846

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