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- EMDB-6038: Electron cryo-microscopy of Kaposi's sarcoma-associated herpesvir... -

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Basic information

Entry
Database: EMDB / ID: EMD-6038
TitleElectron cryo-microscopy of Kaposi's sarcoma-associated herpesvirus virion
Map dataReconstruction of KSHV virion. Capsid-associated tegument proteins around the penton can be visualized at lower contour level (eg, 0.5).
Sample
  • Sample: Kaposi's sarcoma-associated herpesvirus virion
  • Virus: Human herpesvirus 8
KeywordsKSHV / gamma-herpesvirus / capsid structure / capsid-associated tegument protein / the smallest capsid protein / SCP
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / virion component / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
ORF26 / ORF25 / Small capsomere-interacting protein / Core gene UL38 family protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsDai XH / Gong DY / Wu TT / Sun R / Zhou ZH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: CryoEM and mutagenesis reveal that the smallest capsid protein cements and stabilizes Kaposi's sarcoma-associated herpesvirus capsid.
Authors: Xinghong Dai / Danyang Gong / Yuchen Xiao / Ting-Ting Wu / Ren Sun / Z Hong Zhou /
Abstract: With just one eighth the size of the major capsid protein (MCP), the smallest capsid protein (SCP) of human tumor herpesviruses--Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus ...With just one eighth the size of the major capsid protein (MCP), the smallest capsid protein (SCP) of human tumor herpesviruses--Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV)--is vital to capsid assembly, yet its mechanism of action is unknown. Here, by cryoEM of KSHV at 6-Å resolution, we show that SCP forms a crown on each hexon and uses a kinked helix to cross-link neighboring MCP subunits. SCP-null mutation decreased viral titer by 1,000 times and impaired but did not fully abolish capsid assembly, indicating an important but nonessential role of SCP. By truncating the C-terminal half of SCP and performing cryoEM reconstruction, we demonstrate that SCP's N-terminal half is responsible for the observed structure and function whereas the C-terminal half is flexible and dispensable. Serial truncations further highlight the critical importance of the N-terminal 10 aa, and cryoEM reconstruction of the one with six residues truncated localizes the N terminus of SCP in the cryoEM density map and enables us to construct a pseudoatomic model of SCP. Fitting of this SCP model and a homology model for the MCP upper domain into the cryoEM map reveals that SCP binds MCP largely via hydrophobic interactions and the kinked helix of SCP bridges over neighboring MCPs to form noncovalent cross-links. These data support a mechanistic model that tumor herpesvirus SCP reinforces the capsid for genome packaging, thus acting as a cementing protein similar to those found in many bacteriophages.
History
DepositionAug 12, 2014-
Header (metadata) releaseAug 27, 2014-
Map releaseSep 3, 2014-
UpdateMar 14, 2018-
Current statusMar 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6038.tif

Downloads & links

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Map

FileDownload / File: emd_6038.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of KSHV virion. Capsid-associated tegument proteins around the penton can be visualized at lower contour level (eg, 0.5).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 720 pix.
= 1483.2 Å		2.06 Å/pix.
x 720 pix.
= 1483.2 Å		2.06 Å/pix.
x 720 pix.
= 1483.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-10.42774105 - 14.513092990000001
Average (Standard dev.)0.00009846 (±0.99999654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-360-360-540
Dimensions720720720
Spacing720720720
CellA=B=C: 1483.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.062.062.06
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z1483.2001483.2001483.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-360-360-540
NC/NR/NS720720720
D min/max/mean-10.42814.5130.000

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Supplemental data

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Sample components

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Entire : Kaposi's sarcoma-associated herpesvirus virion

EntireName: Kaposi's sarcoma-associated herpesvirus virion
Components
  • Sample: Kaposi's sarcoma-associated herpesvirus virion
  • Virus: Human herpesvirus 8

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Supramolecule #1000: Kaposi's sarcoma-associated herpesvirus virion

SupramoleculeName: Kaposi's sarcoma-associated herpesvirus virion / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 8

SupramoleculeName: Human herpesvirus 8 / type: virus / ID: 1 / Name.synonym: Kaposi's sarcoma-associated herpesvirus / NCBI-ID: 37296 / Sci species name: Human herpesvirus 8 / Sci species strain: BAC16 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Kaposi's sarcoma-associated herpesvirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: capsid / Diameter: 1350 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: 7.4 / Details: PBS
GridDetails: 300-mesh Quantifoil R2/1 copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 80 K
DetailsImages recorded with K2 super-resolution mode.
DateNov 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 8000 / Average electron dose: 25 e/Å2
Details: Every image is the average of 26 frames recorded by the direct electron detector.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 48500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 14000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: IMIRS / Number images used: 20395

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