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- PDB-6od7: Herpes simplex virus type 1 (HSV-1) pUL6 portal protein, dodecame... -

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Entry
Database: PDB / ID: 6od7
TitleHerpes simplex virus type 1 (HSV-1) pUL6 portal protein, dodecameric complex
ComponentsPortal protein
KeywordsVIRAL PROTEIN / DNA-translocation / portal / DNA-packaging / dodecamer
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization => GO:0051276 / virion component => GO:0044423 / viral release from host cell / host cell nucleus / Portal protein
Function and homology information
Biological speciesHuman herpesvirus 1 strain KOS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsLiu, Y.T. / Jih, J. / Dai, X.H. / Bi, G.Q. / Zhou, Z.H.
Funding support China, United States, 9items
OrganizationGrant numberCountry
Other government2017YFA0505300 National Key R&D Program of China. China
Other government2016YFA0400900 National Key R&D Program of China. China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome.
Authors: Yun-Tao Liu / Jonathan Jih / Xinghong Dai / Guo-Qiang Bi / Z Hong Zhou /
Abstract: Herpesviruses are enveloped viruses that are prevalent in the human population and are responsible for diverse pathologies, including cold sores, birth defects and cancers. They are characterized by ...Herpesviruses are enveloped viruses that are prevalent in the human population and are responsible for diverse pathologies, including cold sores, birth defects and cancers. They are characterized by a highly pressurized pseudo-icosahedral capsid-with triangulation number (T) equal to 16-encapsidating a tightly packed double-stranded DNA (dsDNA) genome. A key process in the herpesvirus life cycle involves the recruitment of an ATP-driven terminase to a unique portal vertex to recognize, package and cleave concatemeric dsDNA, ultimately giving rise to a pressurized, genome-containing virion. Although this process has been studied in dsDNA phages-with which herpesviruses bear some similarities-a lack of high-resolution in situ structures of genome-packaging machinery has prevented the elucidation of how these multi-step reactions, which require close coordination among multiple actors, occur in an integrated environment. To better define the structural basis of genome packaging and organization in herpes simplex virus type 1 (HSV-1), we developed sequential localized classification and symmetry relaxation methods to process cryo-electron microscopy (cryo-EM) images of HSV-1 virions, which enabled us to decouple and reconstruct hetero-symmetric and asymmetric elements within the pseudo-icosahedral capsid. Here we present in situ structures of the unique portal vertex, genomic termini and ordered dsDNA coils in the capsid spooled around a disordered dsDNA core. We identify tentacle-like helices and a globular complex capping the portal vertex that is not observed in phages, indicative of herpesvirus-specific adaptations in the DNA-packaging process. Finally, our atomic models of portal vertex elements reveal how the fivefold-related capsid accommodates symmetry mismatch imparted by the dodecameric portal-a longstanding mystery in icosahedral viruses-and inform possible DNA-sequence recognition and headful-sensing pathways involved in genome packaging. This work showcases how to resolve symmetry-mismatched elements in a large eukaryotic virus and provides insights into the mechanisms of herpesvirus genome packaging.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


Theoretical massNumber of molelcules
Total (without water)889,95012
Polymers889,95012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area62630 Å2
ΔGint-222 kcal/mol
Surface area228140 Å2

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Components

#1: Protein
Portal protein


Mass: 74162.523 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: H9E912

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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: Human herpesvirus 1 strain KOS / Type: VIRUS / Details: Cultured in Vero cells. / Entity ID: all / Source: NATURAL
Molecular weightValue: 200 MDa / Experimental value: NO
Source (natural)Organism: Human herpesvirus 1 strain KOS
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 1300 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 298 K
Details: The sample was manually blotted and frozen with a homemade plunger.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 14000 X / Calibrated magnification: 24271 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 79 K
Image recordingAverage exposure time: 13 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8000
Image scansSampling size: 2.5 µm / Width: 1440 / Height: 1440 / Movie frames/image: 26

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND3CTF correction
5RELION2.1CTF correction
8Coot0.8.6.1model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
14PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 45445
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39939 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 250 / Protocol: AB INITIO MODEL / Space: REAL
Details: Ab initio models were built in Coot, and then iteratively refined between real space refinement in PHENIX and manual refinement in Coot.
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008237500
ELECTRON MICROSCOPYf_angle_d1.144850988
ELECTRON MICROSCOPYf_chiral_restr0.06485604
ELECTRON MICROSCOPYf_plane_restr0.00886612
ELECTRON MICROSCOPYf_dihedral_angle_d7.375822116

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