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- EMDB-21505: Structures of Capsid and Capsid-Associated Tegument Complex insid... -

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Basic information

Entry
Database: EMDB / ID: EMD-21505
TitleStructures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus
Map dataC5 reconstruction of a portal-containing EBV capsid
Sample
  • Virus: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Biological speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsLiu W / Cui YX / Wang CY / Li ZH / Gong DY / Dai XH / Bi GQ / Sun R / Zhou ZH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, DE025567 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: Nat Microbiol / Year: 2020
Title: Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.
Authors: Wei Liu / Yanxiang Cui / Caiyan Wang / Zihang Li / Danyang Gong / Xinghong Dai / Guo-Qiang Bi / Ren Sun / Z Hong Zhou /
Abstract: As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been ...As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.
History
DepositionMar 3, 2020-
Header (metadata) releaseApr 1, 2020-
Map releaseJul 15, 2020-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21505.png

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Map

FileDownload / File: emd_21505.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC5 reconstruction of a portal-containing EBV capsid
Voxel sizeX=Y=Z: 2.72 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.03159805 - 0.06504002
Average (Standard dev.)0.0037764185 (±0.0072838203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-255-255
Dimensions512512512
Spacing512512512
CellA=B=C: 1392.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.722.722.72
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z1392.6401392.6401392.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162182277
MAP C/R/S123
start NC/NR/NS-255-255-255
NC/NR/NS512512512
D min/max/mean-0.0320.0650.004

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Supplemental data

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Sample components

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Entire : Human herpesvirus 4 strain B95-8

EntireName: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Components
  • Virus: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))

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Supramolecule #1: Human herpesvirus 4 strain B95-8

SupramoleculeName: Human herpesvirus 4 strain B95-8 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10377 / Sci species name: Human herpesvirus 4 strain B95-8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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 buffer, pH 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: The grids were manually plunged into the ethane..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1833 / Average electron dose: 28.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: 3D reconstruction of portal-containing particles
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1959

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