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- EMDB-74419: Human cytomegalovirus UL52 4-mer -

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Basic information

Entry
Database: EMDB / ID: EMD-74419
TitleHuman cytomegalovirus UL52 4-mer
Map dataHCMV UL52 4-mer
Sample
  • Complex: UL52
    • Protein or peptide: Packaging protein UL32 homolog
  • Ligand: ZINC ION
KeywordsHuman cytomegalovirus / HCMV / viral genome packaging / packaging accessory factor / UL52 / VIRAL PROTEIN
Function / homologyHerpesvirus major envelope glycoprotein / Herpesvirus putative major envelope glycoprotein / Herpesviridae UL32 packaging protein family profile. / host cell cytoplasm / viral envelope / host cell nucleus / zinc ion binding / Packaging protein UL32 homolog
Function and homology information
Biological speciesHuman betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsBailey EJ / Devarkar SC / Xiong Y / Didychuk AL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2 AI171113 United States
American Cancer SocietyPF-24-1322561-01-RMC United States
CitationJournal: bioRxiv / Year: 2026
Title: Conserved assembly architecture of the essential herpesvirus packaging accessory factor.
Authors: Elizabeth J Bailey / Swapnil C Devarkar / Renata Szczepaniak / Laura M Meißner / Xinyu Chen / Chunxiang Wu / Sandra K Weller / Yong Xiong / Allison L Didychuk /
Abstract: To create a new wave of infectious virions, all herpesviruses require an accessory factor of unknown function to package their viral genomes into nascent capsids. Here, we present cryo-EM structures ...To create a new wave of infectious virions, all herpesviruses require an accessory factor of unknown function to package their viral genomes into nascent capsids. Here, we present cryo-EM structures of the packaging accessory factor from the α-herpesvirus herpes simplex virus type 1 (HSV-1, UL32) and the β-herpesvirus human cytomegalovirus (HCMV, UL52). Unlike homologs from the γ-herpesviruses, neither UL32 nor UL52 form stable homopentameric rings. UL52 forms incomplete pentameric rings lacking one or two protomers. UL32 does not form stable higher-order species, but stabilization through chemical crosslinking revealed a novel quaternary structure where three pentameric rings assemble into a "tripentamer." Our results reveal that herpesvirus packaging accessory factors adopt distinct oligomeric states but are constrained to pentameric symmetry. Assembly of protomers into a ring creates a positively charged central channel that we show is critical for infectious virus production in HSV-1. Taken together, our study points to a structurally conserved, essential function of packaging accessory factors across the .
History
DepositionDec 9, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74419.png

Downloads & links

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Map

FileDownload / File: emd_74419.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHCMV UL52 4-mer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.11092327 - 0.30320442
Average (Standard dev.)0.00029212603 (±0.006662405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A

Fileemd_74419_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_74419_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UL52

EntireName: UL52
Components
  • Complex: UL52
    • Protein or peptide: Packaging protein UL32 homolog
  • Ligand: ZINC ION

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Supramolecule #1: UL52

SupramoleculeName: UL52 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human betaherpesvirus 5

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Macromolecule #1: Packaging protein UL32 homolog

MacromoleculeName: Packaging protein UL32 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 74.23968 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNPSTHVSSN GPTTPPHGPH TTFLPPTSPA PSTSSVAAAT LCSPQRQAVS RYSGWSTEYT QWHSDLTTEL LWHAHPRQVP MDEALAAAA AASYQVNPQH PANRYRHYEF QTLSLGTSEV DELLNCCAEE TTCGGTQSTV LTNATNTTNC GGAVAGSSNA G PAGASAAC ...String:
MNPSTHVSSN GPTTPPHGPH TTFLPPTSPA PSTSSVAAAT LCSPQRQAVS RYSGWSTEYT QWHSDLTTEL LWHAHPRQVP MDEALAAAA AASYQVNPQH PANRYRHYEF QTLSLGTSEV DELLNCCAEE TTCGGTQSTV LTNATNTTNC GGAVAGSSNA G PAGASAAC DLDAELAGLE TSAADFEQLR RLCAPLAIDT RCNLCAIISI CLKQDCDQSW LLEYSLLCFK CSYAPRAALS TL IIMSEFT HLLQQHFSDL RIDDLFRHHV LTVFDFHLHF FINRCFEKQV GDAVDNENVT LNHLAVVRAM VMGEDTVPYN KPR RHPQQK QKTNPYHVEV PQELIDNFLE HSSPSRDRFV QLLFYMWAGT GVMSTTPLTE LTHTKFARLD ALSTTSERED ARMM MEEEE DEEGGEKGGD DPGRHNGGGT SGGFSESTLK KNVGPIYLCP VPAFFTKNQT STVCLLCELM ACSYYDNVVL RELYR RVVS YCQNNVKMVD RIQLVLADLL RECTSPLGAA HEDVARCGLE APTSPGGDSD YHGLSGVDGA LARPDPVFCH VLRQAG VTG IYKHFFCDPQ CAGNIRVTNE AVLFGRLHPH HVQEVKLAIC HDNYYISRLP RRVWLCITLF KAFQITKRTY KGKVHLA DF MRDFTQLLES CDIKLVDPTY VIDKYV

UniProtKB: Packaging protein UL32 homolog

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.55 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES pH 7.6
100.0 mMNaClsodium chloride
1.0 mMC4H10O2S2dithiothreitol (DTT)
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa / Details: 11 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 146592
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9zm2:
Human cytomegalovirus UL52 4-mer

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