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- EMDB-1354: Allosteric signaling and a nuclear exit strategy: binding of UL25... -

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Basic information

Entry
Database: EMDB / ID: EMD-1354
TitleAllosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids.
Map dataEM Map from HSV-1 C-capsids
Sample
  • Sample: HSV-1 C-capsids
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.9 Å
AuthorsTrus BL / Newcomb WW / Cheng N / Cardone G / Marekov L / Homa FL / Brown JC / Steven AC
CitationJournal: Mol Cell / Year: 2007
Title: Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids.
Authors: Benes L Trus / William W Newcomb / Naiqian Cheng / Giovanni Cardone / Lyuben Marekov / Fred L Homa / Jay C Brown / Alasdair C Steven /
Abstract: UL25 and UL17 are two essential minor capsid proteins of HSV-1, implicated in DNA packaging and capsid maturation. We used cryo-electron microscopy to examine their binding to capsids, whose ...UL25 and UL17 are two essential minor capsid proteins of HSV-1, implicated in DNA packaging and capsid maturation. We used cryo-electron microscopy to examine their binding to capsids, whose architecture observes T = 16 icosahedral geometry. C-capsids (mature DNA-filled capsids) have an elongated two-domain molecule present at a unique, vertex-adjacent site that is not seen at other quasiequivalent sites or on unfilled capsids. Using SDS-PAGE and mass spectrometry to analyze wild-type capsids, UL25 null capsids, and denaturant-extracted capsids, we conclude that (1) the C-capsid-specific component is a heterodimer of UL25 and UL17, and (2) capsids have additional populations of UL25 and UL17 that are invisible in reconstructions because of sparsity and/or disorder. We infer that binding of the ordered population reflects structural changes induced on the outer surface as pressure builds up inside the capsid during DNA packaging. Its binding may signal that the C-capsid is ready to exit the nucleus.
History
DepositionApr 6, 2007-
Header (metadata) releaseApr 24, 2007-
Map releaseApr 24, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 130
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 130
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1354.gif

Downloads & links

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Map

FileDownload / File: emd_1354.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM Map from HSV-1 C-capsids
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.68 Å/pix.
x 360 pix.
= 1324.8 Å		3.68 Å/pix.
x 360 pix.
= 1324.8 Å		3.68 Å/pix.
x 360 pix.
= 1324.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.68 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 83.5 / Movie #1: 130
Minimum - Maximum-516.261999999999944 - 552.66700000000003
Average (Standard dev.)28.8185 (±89.440200000000004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 1324.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.683.683.68
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z1324.8001324.8001324.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-516.262552.66728.819

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Supplemental data

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Sample components

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Entire : HSV-1 C-capsids

EntireName: HSV-1 C-capsids
Components
  • Sample: HSV-1 C-capsids
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1000: HSV-1 C-capsids

SupramoleculeName: HSV-1 C-capsids / 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 / NCBI-ID: 10298 / Sci species name: Human herpesvirus 1 / 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 / Name: HSV-1 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

Concentration0.25 mg/mL
BufferpH: 7.5
Details: 0.01 M Tris-HCl, 0.5 M NaCl, 1 mM EDTA, pH 7.5 (This is the buffer we call TNE.)
GridDetails: none
VitrificationCryogen name: ETHANE / Chamber humidity: 20 % / Chamber temperature: 93.15 K / Instrument: LEICA KF80
Details: Vitrification instrument: Reichert-Jung KF80. Vitrification carried out in nitrogen atmosphere
Method: 4 microliter sample dropped onto grid, blotted on one side for 1.5 seconds

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
TemperatureMin: 88.15 K / Max: 98.15 K / Average: 93.15 K
Alignment procedureLegacy - Astigmatism: 300000
DateMar 5, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 3.68 µm / Number real images: 1828 / Average electron dose: 12 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.05 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle, phase reversal
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT2, EM3DR2 / Number images used: 1286
Final two d classificationNumber classes: 1

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