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- EMDB-22168: Cryo-EM structure of EBV BFLF1 -

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Basic information

Entry
Database: EMDB / ID: EMD-22168
TitleCryo-EM structure of EBV BFLF1
Map data
SampleDecamer structure of EBV BFLF1
  • Packaging protein UL32Packaging and labeling
  • ligand
Function / homologyHerpesvirus major envelope glycoprotein / viral envelope / host cell cytoplasm / host cell nucleus / cytoplasm / Packaging protein UL32
Function and homology information
Biological speciesEpstein-Barr virus (strain GD1) (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDidychuk AL / Gates SN / Martin A / Glaunsinger B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI122528 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2021
Title: A pentameric protein ring with novel architecture is required for herpesviral packaging.
Authors: Allison L Didychuk / Stephanie N Gates / Matthew R Gardner / Lisa M Strong / Andreas Martin / Britt A Glaunsinger /
Abstract: Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids, which involves essential accessory factors that are poorly ...Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids, which involves essential accessory factors that are poorly understood. Here, we present structures of two such accessory factors from the oncogenic herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV; ORF68) and Epstein-Barr virus (EBV; BFLF1). These homologous proteins form highly similar homopentameric rings with a positively charged central channel that binds double-stranded DNA. Mutation of individual positively charged residues within but not outside the channel ablates DNA binding, and in the context of KSHV infection, these mutants fail to package the viral genome or produce progeny virions. Thus, we propose a model in which ORF68 facilitates the transfer of newly replicated viral genomes to the packaging motor.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 15, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0281
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0281
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xfa
  • Surface level: 0.0281
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22168.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 256 pix.
= 291.84 Å
1.14 Å/pix.
x 256 pix.
= 291.84 Å
1.14 Å/pix.
x 256 pix.
= 291.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density
Contour LevelBy AUTHOR: 0.0281 / Movie #1: 0.0281
Minimum - Maximum-0.071760505 - 0.12694223
Average (Standard dev.)0.00026288128 (±0.0044496018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 291.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z291.840291.840291.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0720.1270.000

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Supplemental data

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Sample components

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Entire Decamer structure of EBV BFLF1

EntireName: Decamer structure of EBV BFLF1 / Number of components: 3

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Component #1: protein, Decamer structure of EBV BFLF1

ProteinName: Decamer structure of EBV BFLF1 / Recombinant expression: No
MassTheoretical: 536 kDa
SourceSpecies: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Packaging protein UL32

ProteinName: Packaging protein UL32Packaging and labeling / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 53.678797 kDa
SourceSpecies: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 20 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/mL / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 90 % / Details: 2 second blot, 3 second wait.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 839

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D5 (2x5 fold dihedral) / Number of projections: 32272
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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