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- EMDB-74415: Unknown entry -

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Basic information

Entry
Database: EMDB / ID: EMD-74415
TitleHSV-1 UL32 tripentamer
Map dataHSV-1 UL32 tripentamer
Sample
  • Complex: UL32
    • Protein or peptide: Packaging protein UL32
  • Ligand: ZINC ION
KeywordsHerpes simplex virus type 1 / HSV-1 / viral genome packaging / packaging accessory factor / UL32 / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 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_74415.png

Downloads & links

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Map

FileReleased
AnnotationHSV-1 UL32 tripentamer
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08158495 - 0.26459125
Average (Standard dev.)0.0007165674 (±0.010456848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74415_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UL32

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

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Supramolecule #1: UL32

SupramoleculeName: UL32 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human alphaherpesvirus 1 strain 17

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Macromolecule #1: Packaging protein UL32

MacromoleculeName: Packaging protein UL32 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 63.99377 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATSPPGVLA SVAVCEESPG SSWKAGAFER AYVAFDPSLL ALNEALCAEL LAASHVIGVP PVGTLDEDVA ADVVTAPSRA RGGAGDGGG SGGRGGPRNP PPDPCGEGLL DTGPFSAAAI DTFALDRPCL VCRTIELYKQ TYRLSPQWVA DYAFLCAKCL G APHCAASI ...String:
MATSPPGVLA SVAVCEESPG SSWKAGAFER AYVAFDPSLL ALNEALCAEL LAASHVIGVP PVGTLDEDVA ADVVTAPSRA RGGAGDGGG SGGRGGPRNP PPDPCGEGLL DTGPFSAAAI DTFALDRPCL VCRTIELYKQ TYRLSPQWVA DYAFLCAKCL G APHCAASI FVAAFEFVYV MDRHFLRTKK ATLVGSFARF ALTINDIHRH FFLHCCFRTD GGVPGRHAQK QPKPSPSPGA AK VQYSNYS FLAQSATRAL IGTLASGGEE GAGSAAGSGT QPSLTTALMN WKDCARLLDC TEGRRGGGDS CCTRAAARNG EFE TVAGDR EPEESPDTWA YADLVLLLLA GTPAVWESGP QLRAAAEARR ATVRQSWEAH RGARTRDVAP RFAQFTEPDA QPDL DLGPL MATVLKHGRG RGRTGGECLL CNLLLVRAYW LALRRLRASV VRYSENNTSL FDCIVPVVDQ LEADPETQPG DGGRF VSLL RAAGPEAIFK HMFCDPMCAI TEMEVDPWVL FGHPPATHPD ELLLHKAKLA CGNEFEGRVC IALRALIYTF KTYQVF VPK PTALATFVRE AGALLRRHSI SLLSLEHTLC TYV

UniProtKB: Packaging protein UL32

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 45 / 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

Concentration1.02 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
SoftwareName: EPU
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: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 89851
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-9zly:
HSV-1 UL32 tripentamer

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