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- PDB-9opc: Herpes simplex virus type 1 (HSV-1) C-capsid pUL6 portal protein,... -

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Open data


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Basic information

Entry
Database: PDB / ID: 9opc
TitleHerpes simplex virus type 1 (HSV-1) C-capsid pUL6 portal protein, dodecameric complex
ComponentsCapsid portal protein
KeywordsVIRAL PROTEIN / Complex
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / virion component / host cell nucleus / Capsid portal protein
Function and homology information
Biological speciesHuman alphaherpesvirus 1 strain KOS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsCrofut, E.H. / Kashyap, S. / Stevens, A. / Jih, J. / Liu, Y.-T. / Zhou, Z.H.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151055 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5T32AR071307 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM145388 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
CitationJournal: To Be Published / Year: 2025
Title: Structure of a new capsid form and comparison with A-, B- and C-capsids clarify herpesvirus assembly
Authors: Stevens, A. / Kashyap, S. / Crofut, E.H. / Alvarez-Cabrera, A.L. / Jih, J. / Liu, Y.-T. / Zhou, Z.H.
History
DepositionMay 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Data collection / Database references / Category: citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Capsid portal protein
b: Capsid portal protein
c: Capsid portal protein
d: Capsid portal protein
e: Capsid portal protein
f: Capsid portal protein
g: Capsid portal protein
h: Capsid portal protein
i: Capsid portal protein
j: Capsid portal protein
k: Capsid portal protein
l: Capsid portal protein


Theoretical massNumber of molelcules
Total (without water)890,14212
Polymers890,14212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Capsid portal protein / UL6


Mass: 74178.523 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human alphaherpesvirus 1 strain KOS / References: UniProt: H9E912
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: Dodecameric complex of pUL6 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9PHENIX1.21.2_5419:model refinement
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232140 / Symmetry type: POINT

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