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- EMDB-6213: CryoEM reconstruction of Kaposi's sarcoma-associated herpesvirus ... -

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Entry
Database: EMDB / ID: EMD-6213
TitleCryoEM reconstruction of Kaposi's sarcoma-associated herpesvirus mutant with C-terminal half of SCP truncated (KSHV-SCPN86)
Map dataCryoEM reconstruction of KSHV-SCPN86 mutant. The capsid structure is essentially identical to that of wild-type KSHV.
Sample
  • Sample: Kaposi's sarcoma-associated herpesvirus (KSHV) mutant with the C-terminal half of the smallest capsid protein (SCP) truncated
  • Virus: Human herpesvirus 8
Keywordsherpesvirus / gammaherpesvirus / the smallest capsid protein / cementing protein
Biological speciesHuman herpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsDai XH / Gong DY / Xiao YC / 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
DepositionDec 8, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseFeb 4, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6213.tif

Downloads & links

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Map

FileDownload / File: emd_6213.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of KSHV-SCPN86 mutant. The capsid structure is essentially identical to that of wild-type KSHV.
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: 2.0 / Movie #1: 2
Minimum - Maximum-9.45171356 - 13.47563362
Average (Standard dev.)0.00630803 (±0.92341071)
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
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS-360-360-540
NC/NR/NS720720720
D min/max/mean-9.45213.4760.006

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Supplemental data

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Sample components

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Entire : Kaposi's sarcoma-associated herpesvirus (KSHV) mutant with the C-...

EntireName: Kaposi's sarcoma-associated herpesvirus (KSHV) mutant with the C-terminal half of the smallest capsid protein (SCP) truncated
Components
  • Sample: Kaposi's sarcoma-associated herpesvirus (KSHV) mutant with the C-terminal half of the smallest capsid protein (SCP) truncated
  • Virus: Human herpesvirus 8

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Supramolecule #1000: Kaposi's sarcoma-associated herpesvirus (KSHV) mutant with the C-...

SupramoleculeName: Kaposi's sarcoma-associated herpesvirus (KSHV) mutant with the C-terminal half of the smallest capsid protein (SCP) truncated
type: sample / ID: 1000 / Oligomeric state: icosahedral virus / 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
Details: The smallest capsid protein (SCP) of the virus is truncated at residue number 86.
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: Quantifoil R2/1-Cu200
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsK2 camera super-resolution mode
DateNov 5, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 1184 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
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: 3.0 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: 7.4 Å / Resolution method: OTHER / Software - Name: IMIRS, EMAN1 / Number images used: 1500

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