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- EMDB-22208: CryoET averages of NEC forming hexameric lattices in the presence... -

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Basic information

Entry
Database: EMDB / ID: EMD-22208
TitleCryoET averages of NEC forming hexameric lattices in the presence of membranes (vesicle bilayer)
Map dataCryoET averages of NEC forming hexameric lattices in the presence of vesicle bilayer.
Sample
  • Complex: viral nuclear egress complex (NEC)
Biological speciesE. coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsZhang JJ / Draganova EB
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM126760 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI147625 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111795 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD018111 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Elife / Year: 2020
Title: Structural basis for capsid recruitment and coat formation during HSV-1 nuclear egress.
Authors: Elizabeth B Draganova / Jiayan Zhang / Z Hong Zhou / Ekaterina E Heldwein /
Abstract: During herpesvirus infection, egress of nascent viral capsids from the nucleus is mediated by the viral nuclear egress complex (NEC). NEC deforms the inner nuclear membrane (INM) around the capsid by ...During herpesvirus infection, egress of nascent viral capsids from the nucleus is mediated by the viral nuclear egress complex (NEC). NEC deforms the inner nuclear membrane (INM) around the capsid by forming a hexagonal array. However, how the NEC coat interacts with the capsid and how curved coats are generated to enable budding is yet unclear. Here, by structure-guided truncations, confocal microscopy, and cryoelectron tomography, we show that binding of the capsid protein UL25 promotes the formation of NEC pentagons rather than hexagons. We hypothesize that during nuclear budding, binding of UL25 situated at the pentagonal capsid vertices to the NEC at the INM promotes formation of NEC pentagons that would anchor the NEC coat to the capsid. Incorporation of NEC pentagons at the points of contact with the vertices would also promote assembly of the curved hexagonal NEC coat around the capsid, leading to productive egress of UL25-decorated capsids.
History
DepositionJun 23, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateJul 8, 2020-
Current statusJul 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22208.png

Downloads & links

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Map

FileDownload / File: emd_22208.map.gz / Format: CCP4 / Size: 729.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoET averages of NEC forming hexameric lattices in the presence of vesicle bilayer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.1 Å/pix.
x 72 pix.
= 367.2 Å		5.1 Å/pix.
x 36 pix.
= 183.6 Å		5.1 Å/pix.
x 72 pix.
= 367.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.05 / Movie #1: 1.05
Minimum - Maximum-3.8465462 - 3.7077012
Average (Standard dev.)0.705088400 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-18-36-36
Dimensions367272
Spacing723672
CellA: 367.19998 Å / B: 183.59999 Å / C: 367.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.15.15.1
M x/y/z723672
origin x/y/z0.0000.0000.000
length x/y/z367.200183.600367.200
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS-36-18-36
NC/NR/NS723672
D min/max/mean-3.8473.7080.000

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Supplemental data

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Sample components

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Entire : viral nuclear egress complex (NEC)

EntireName: viral nuclear egress complex (NEC)
Components
  • Complex: viral nuclear egress complex (NEC)

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Supramolecule #1: viral nuclear egress complex (NEC)

SupramoleculeName: viral nuclear egress complex (NEC) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: E. coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 580 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 1.64 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1500
ExtractionNumber tomograms: 1 / Number images used: 3078
Details: The authors' group has resolved the structure and published the result, this experiment serves as a control. Therefore, only one of the ten tomograms was selected randomly to do the ...Details: The authors' group has resolved the structure and published the result, this experiment serves as a control. Therefore, only one of the ten tomograms was selected randomly to do the subtomograms extraction and the subsequent sub-tomographic averaging.
Final angle assignmentType: ANGULAR RECONSTITUTION

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