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- EMDB-31295: Human Cytomegalovirus, the reconstruction of C12 portal in the en... -

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Basic information

Entry
Database: EMDB / ID: EMD-31295
TitleHuman Cytomegalovirus, the reconstruction of C12 portal in the enveloped capsid
Map data
Sample
  • Virus: Human betaherpesvirus 5
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / virion component / host cell nucleus / Capsid portal protein
Function and homology information
Biological speciesHuman betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLi Z / Pang J / Dong L / Yu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for genome packaging, retention, and ejection in human cytomegalovirus.
Authors: Zhihai Li / Jingjing Pang / Lili Dong / Xuekui Yu /
Abstract: How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched ...How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched portal and the capsid vertex-specific components (CVSCs) of HCMV. The 5-fold symmetric 10-helix anchor-uncommon among known portals-contacts the portal-encircling DNA, which is presumed to squeeze the portal as the genome packaging proceeds. We surmise that the 10-helix anchor dampens this action to delay the portal reaching a "head-full" packaging state, thus facilitating the large genome to be packaged. The 6-fold symmetric turret, latched via a coiled coil to a helix from a major capsid protein, supports the portal to retain the packaged genome. CVSCs at the penton vertices-presumed to increase inner capsid pressure-display a low stoichiometry, which would aid genome retention. We also demonstrate that the portal and capsid undergo conformational changes to facilitate genome ejection after viral cell entry.
History
DepositionMay 12, 2021-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateAug 18, 2021-
Current statusAug 18, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31295.png

Downloads & links

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Map

FileDownload / File: emd_31295.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.63 Å/pix.
x 112 pix.
= 182. Å		1.63 Å/pix.
x 112 pix.
= 182. Å		1.63 Å/pix.
x 112 pix.
= 182. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.13315177 - 0.12248281
Average (Standard dev.)0.0048299483 (±0.013023421)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 182.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6251.6251.625
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z182.000182.000182.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ112112112
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS112112112
D min/max/mean-0.1330.1220.005

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Supplemental data

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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: 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: 7.5
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22087
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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