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- EMDB-1904: Labeling and Localization of the Herpes Simplex Virus Capsid Prot... -

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Entry
Database: EMDB / ID: EMD-1904
TitleLabeling and Localization of the Herpes Simplex Virus Capsid Protein UL25 and Its Interaction with the Two Triplexes Closest to the Penton.
Map dataSurface rendered view of HSV-1 C-capsid where protein UL25 has been genetically tagged with GFP at amino acid 50.
Sample
  • Sample: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
  • Virus: Human herpesvirus 1 strain KOS
KeywordsHSV-1 / capsid / UL25 / cryo-EM
Biological speciesHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 13.7 Å
AuthorsConway JF / Cockrell SK / Copeland AM / Newcomb WW / Brown JC / Homa FL
CitationJournal: J Mol Biol / Year: 2010
Title: Labeling and localization of the herpes simplex virus capsid protein UL25 and its interaction with the two triplexes closest to the penton.
Authors: James F Conway / Shelley K Cockrell / Anna Maria Copeland / William W Newcomb / Jay C Brown / Fred L Homa /
Abstract: The herpes simplex virus type 1 UL25 protein is one of seven viral proteins that are required for DNA cleavage and packaging. Together with UL17, UL25 forms part of an elongated molecule referred to ...The herpes simplex virus type 1 UL25 protein is one of seven viral proteins that are required for DNA cleavage and packaging. Together with UL17, UL25 forms part of an elongated molecule referred to as the C-capsid-specific component (CCSC). Five copies of the CCSC are located at each of the capsid vertices on DNA-containing capsids. To study the conformation of UL25 as it is folded on the capsid surface, we identified the sequence recognized by a UL25-specific monoclonal antibody and localized the epitope on the capsid surface by immunogold electron microscopy. The epitope mapped to amino acids 99-111 adjacent to the region of the protein (amino acids 1-50) that is required for capsid binding. In addition, cryo-EM reconstructions of C-capsids in which the green fluorescent protein (GFP) was fused within the N-terminus of UL25 localized the point of contact between UL25 and GFP. The result confirmed the modeled location of the UL25 protein in the CCSC density as the region that is distal to the penton with the N-terminus of UL25 making contact with the triplex one removed from the penton. Immunofluorescence experiments at early times during infection demonstrated that UL25-GFP was present on capsids located within the cytoplasm and adjacent to the nucleus. These results support the view that UL25 is present on incoming capsids with the capsid-binding domain of UL25 located on the surface of the mature DNA-containing capsid.
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: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1904.png

Downloads & links

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Map

FileDownload / File: emd_1904.map.gz / Format: CCP4 / Size: 985.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendered view of HSV-1 C-capsid where protein UL25 has been genetically tagged with GFP at amino acid 50.
Voxel sizeX=Y=Z: 2.12 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-3.73272991 - 4.35211754
Average (Standard dev.)-0.00000001 (±0.99999994)
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-3.7334.352-0.000

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Supplemental data

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Sample components

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Entire : HSV-1 C-capsid with protein UL25 genetically labeled with GFP at ...

EntireName: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
Components
  • Sample: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
  • Virus: Human herpesvirus 1 strain KOS

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Supramolecule #1000: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at ...

SupramoleculeName: HSV-1 C-capsid with protein UL25 genetically labeled with GFP 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: OTHER / Instrument: FEI VITROBOT MARK III
Details: Vitrification instrument: Vitrobot mark III. Cryogen was an equal mix of ethane-propane.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 29000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Bits/pixel: 8
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: 13.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM

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