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Yorodumi- PDB-6od7: Herpes simplex virus type 1 (HSV-1) pUL6 portal protein, dodecame... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6od7 | ||||||||||||||||||||||||||||||
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Title | Herpes simplex virus type 1 (HSV-1) pUL6 portal protein, dodecameric complex | ||||||||||||||||||||||||||||||
Components | Portal protein | ||||||||||||||||||||||||||||||
Keywords | VIRAL PROTEIN / DNA-translocation / portal / DNA-packaging / dodecamer | ||||||||||||||||||||||||||||||
Function / homology | Herpesvirus 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 species | Human herpesvirus 1 strain KOS | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å | ||||||||||||||||||||||||||||||
Authors | Liu, Y.T. / Jih, J. / Dai, X.H. / Bi, G.Q. / Zhou, Z.H. | ||||||||||||||||||||||||||||||
Funding support | China, United States, 9items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6od7.cif.gz | 831.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6od7.ent.gz | 669.9 KB | Display | PDB format |
PDBx/mmJSON format | 6od7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6od7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6od7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6od7_validation.xml.gz | 125.3 KB | Display | |
Data in CIF | 6od7_validation.cif.gz | 189.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/6od7 ftp://data.pdbj.org/pub/pdb/validation_reports/od/6od7 | HTTPS FTP |
-Related structure data
Related structure data | 9862MC 9860C 9861C 9863C 9864C 6odmC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human herpesvirus 1 strain KOS / Type: VIRUS / Details: Cultured in Vero cells. / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 200 MDa / Experimental value: NO |
Source (natural) | Organism: Human herpesvirus 1 strain KOS |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Virus shell | Name: Capsid / Diameter: 1300 nm / Triangulation number (T number): 16 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 298 K Details: The sample was manually blotted and frozen with a homemade plunger. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 14000 X / Calibrated magnification: 24271 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 79 K |
Image recording | Average 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 scans | Sampling size: 2.5 µm / Width: 1440 / Height: 1440 / Movie frames/image: 26 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 45445 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C12 (12 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39939 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B 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. | ||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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