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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
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: Bailey EJ / Devarkar SC / Szczepaniak R / Meissner LM / Chen X / Wu C / Weller SK / Xiong Y / Didychuk AL
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

FileReleased
AnnotationHCMV UL52 4-mer
Voxel sizeX=Y=Z: 1.07 Å
Density
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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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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