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- EMDB-34692: C12 portal in HCMV A-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-34692
TitleC12 portal in HCMV A-capsid
Map data
Sample
  • Virus: Human betaherpesvirus 5
    • Protein or peptide: Portal protein
KeywordsA-capsid / portal / in-situ structure / VIRUS / 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 herpesvirus 5 strain AD169 / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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 8, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34692.png

Downloads & links

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Map

FileDownload / File: emd_34692.map.gz / Format: CCP4 / Size: 8 MB / 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 128 pix.
= 208. Å		1.63 Å/pix.
x 128 pix.
= 208. Å		1.63 Å/pix.
x 128 pix.
= 208. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.625 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0185
Minimum - Maximum-0.06713662 - 0.07675392
Average (Standard dev.)0.0025050717 (±0.007826969)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_34692_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_34692_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
    • 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: No / Virus empty: Yes

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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 herpesvirus 5 strain AD169 / Strain: AD169
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: 7.4
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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