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- EMDB-34698: Icosahedral reconstruction of HCMV A-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-34698
TitleIcosahedral reconstruction of HCMV A-capsid
Map data
Sample
  • Virus: Human betaherpesvirus 5
KeywordsA-capsid / icosahedral recontruction / VIRUS
Biological speciesHuman betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLi Z / Yu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-electron microscopy structures of capsids and in situ portals of DNA-devoid capsids of human cytomegalovirus.
Authors: Zhihai Li / Jingjing Pang / Rongchao Gao / Qingxia Wang / Maoyan Zhang / Xuekui Yu /
Abstract: The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold ...The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold interaction and the conformational changes that occur to the portal during the different stages of capsid formation have yet to be elucidated structurally. Here we present high-resolution structures of the A- and B-capsids and in-situ portals of human cytomegalovirus. We show that scaffolds bind to the hydrophobic cavities formed by the dimerization and Johnson-fold domains of the major capsid proteins. We further show that 12 loop-helix-loop fragments-presumably from the scaffold domain-insert into the hydrophobic pocket of the portal crown domain. The portal also undergoes significant changes both positionally and conformationally as it accompanies DNA packaging. These findings unravel the mechanism by which the portal interacts with the scaffold to nucleate capsid assembly and further our understanding of scaffold expulsion and DNA incorporation.
History
DepositionNov 9, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34698.png

Downloads & links

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Map

FileDownload / File: emd_34698.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 1024 pix.
= 1664. Å		1.63 Å/pix.
x 1024 pix.
= 1664. Å		1.63 Å/pix.
x 1024 pix.
= 1664. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.625 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.027708977 - 0.058095865
Average (Standard dev.)0.00018100085 (±0.003566976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions102410241024
Spacing102410241024
CellA=B=C: 1664.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34698_msk_1.map
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Half map: #2

Fileemd_34698_half_map_1.map
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Half map: #1

Fileemd_34698_half_map_2.map
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Sample components

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Entire : Human betaherpesvirus 5

EntireName: Human betaherpesvirus 5
Components
  • Virus: Human betaherpesvirus 5

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Supramolecule #1: Human betaherpesvirus 5

SupramoleculeName: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10359 / Sci species name: Human betaherpesvirus 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25502
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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