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- EMDB-31296: Human Cytomegalovirus, C12 portal -

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Basic information

Entry
Database: EMDB / ID: EMD-31296
TitleHuman Cytomegalovirus, C12 portal
Map data
Sample
  • Virus: Human betaherpesvirus 5
    • Protein or peptide: Portal protein
KeywordsC12 portal / partially-enveloped capsid / Human Cytomegalovirus / VIRAL PROTEIN
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / virion component / host cell nucleus / Capsid portal protein
Function and homology information
Biological speciesHuman cytomegalovirus / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi Z / Yu X / Dong L
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-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7et2
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7et2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31296.png

Downloads & links

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Map

FileDownload / File: emd_31296.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 128 pix.
= 208. Å		1.63 Å/pix.
x 128 pix.
= 208. Å		1.63 Å/pix.
x 128 pix.
= 208. 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: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.040209487 - 0.086990125
Average (Standard dev.)0.013550217 (±0.0068225767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6251.6251.625
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0400.0870.014

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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
    • Protein or peptide: Portal protein

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Supramolecule #1: Human betaherpesvirus 5

SupramoleculeName: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus
Molecular weightTheoretical: 78.634805 KDa
SequenceString: MERNHWNEKS SGAKRSRERD LTLSTIRSIL AADERLRIKA SSYLGVGRGV DDEAVIDIFP TGQTMSFLRL LHGFLGTCRG QSMHQVLRD PCVLRKQLLY GVCKTLFDTI TVRRVAEEWK LHAALFPYRA LDEEDLEQYL LVWSASLRQS VQTGVLGALR D ILYQYADN ...String:
MERNHWNEKS SGAKRSRERD LTLSTIRSIL AADERLRIKA SSYLGVGRGV DDEAVIDIFP TGQTMSFLRL LHGFLGTCRG QSMHQVLRD PCVLRKQLLY GVCKTLFDTI TVRRVAEEWK LHAALFPYRA LDEEDLEQYL LVWSASLRQS VQTGVLGALR D ILYQYADN DDYGLYVDWC VTVGLVPLLD VKTKPSEAAE RAQFVRAAVQ RATETHPLAQ DLLQANLALL LQVAERLGAV RV ANAPEVR VFKKVRSERL EAQLRGKHIR LYVAAEPLAY ERDKLLFTTP VAHLHEEILR YDGLCRHQKI CQLLNTFPVK VVT ASRHEL NCKKLVEMME QHDRGSDAKK SIMKFLLNVS DSKSRIGIED SVESFLQDLT PSLVDQNRLL PARGPGGPGV VGPG GAVVG GPAGHVGLLP PPPGPAAPER DIRDLFKKQV IKCLEEQIQS QVDEIQDLRT LNQTWENRVR ELRDLLTRYA SRRED SMSL GARDAELYHL PVLEAVRKAR DAAPFRPLAV EDNRLVANSF FSQFVPGTES LERFLTQLWE NEYFRTFRLR RLVTHQ GAE EAIVYSNYTV ERVTLPYLCH ILALGTLDPV PEAYLQLSFG EIVAAAYDDS KFCRYVELIC SREKARRRQM SREAAGG VP ERGTASSGGP GTLERSAPRR LITADEERRG PERVGRFRNG GPDDPRRAGG PYGFH

UniProtKB: Capsid portal protein

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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

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40903
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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