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- PDB-9zly: HSV-1 UL32 tripentamer -

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Basic information

Entry
Database: PDB / ID: 9zly
TitleHSV-1 UL32 tripentamer
ComponentsPackaging protein UL32
KeywordsVIRAL PROTEIN / Herpes simplex virus type 1 / HSV-1 / viral genome packaging / packaging accessory factor / UL32
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
Function and homology information
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsBailey, E.J. / Devarkar, S.C. / Xiong, Y. / Didychuk, A.L.
Funding support United States, 2items
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, E.J. / Devarkar, S.C. / Szczepaniak, R. / Meissner, L.M. / Chen, X. / Wu, C. / Weller, S.K. / Xiong, Y. / Didychuk, A.L.
History
DepositionDec 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Packaging protein UL32
B: Packaging protein UL32
C: Packaging protein UL32
D: Packaging protein UL32
E: Packaging protein UL32
F: Packaging protein UL32
G: Packaging protein UL32
H: Packaging protein UL32
I: Packaging protein UL32
J: Packaging protein UL32
K: Packaging protein UL32
L: Packaging protein UL32
M: Packaging protein UL32
N: Packaging protein UL32
O: Packaging protein UL32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)962,85060
Polymers959,90715
Non-polymers2,94345
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, native gel electrophoresis, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Packaging protein UL32


Mass: 63993.770 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL32 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10216
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: UL32 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES pH 7.6C8H18N2O4S1
2100 mMsodium chlorideNaCl1
31 mMdithiothreitol (DTT)C4H10O2S21
SpecimenConc.: 1.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 11 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89851 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00261065
ELECTRON MICROSCOPYf_angle_d0.43883010
ELECTRON MICROSCOPYf_dihedral_angle_d3.5628508
ELECTRON MICROSCOPYf_chiral_restr0.0369270
ELECTRON MICROSCOPYf_plane_restr0.00410785

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