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- EMDB-22207: CryoET averages of NEC in the presence of UL25delta44 Q72A -

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Basic information

Entry
Database: EMDB / ID: EMD-22207
TitleCryoET averages of NEC in the presence of UL25delta44 Q72A
Map dataCryoET averages of NEC in the presence of UL25delta44 Q72A
Sample
  • Complex: capsid protein UL25 (residues 45-580)
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: 1.4
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22207.png

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Map

FileDownload / File: emd_22207.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoET averages of NEC in the presence of UL25delta44 Q72A
Voxel sizeX=Y=Z: 10.212 Å
Density
Contour LevelBy AUTHOR: 1.4 / Movie #1: 1.4
Minimum - Maximum-4.543896 - 5.7728004
Average (Standard dev.)-0.00000001567 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-38-38-38
Dimensions767676
Spacing767676
CellA=B=C: 776.11176 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.21210.21210.212
M x/y/z767676
origin x/y/z0.0000.0000.000
length x/y/z776.112776.112776.112
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS-38-38-38
NC/NR/NS767676
D min/max/mean-4.5445.773-0.000

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Supplemental data

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Sample components

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Entire : capsid protein UL25 (residues 45-580)

EntireName: capsid protein UL25 (residues 45-580)
Components
  • Complex: capsid protein UL25 (residues 45-580)

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Supramolecule #1: capsid protein UL25 (residues 45-580)

SupramoleculeName: capsid protein UL25 (residues 45-580) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: E. coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 57 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 29000 / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.64 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 13 / Number images used: 4044
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 4044

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