+Open data
-Basic information
Entry | Database: PDB / ID: 8co6 | ||||||||||||||||||
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Title | Subtomogram average of Immature Rotavirus TLP penton | ||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Rotavirus / STA | ||||||||||||||||||
Function / homology | Function and homology information viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Rotavirus A | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.7 Å | ||||||||||||||||||
Authors | Shah, P.N.M. / Stuart, D.I. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Cell Host Microbe / Year: 2023 Title: Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography. Authors: Pranav N M Shah / James B Gilchrist / Björn O Forsberg / Alister Burt / Andrew Howe / Shyamal Mosalaganti / William Wan / Julika Radecke / Yuriy Chaban / Geoff Sutton / David I Stuart / Mark Boyce / Abstract: Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and ...Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8co6.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8co6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8co6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8co6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8co6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8co6_validation.xml.gz | 249.2 KB | Display | |
Data in CIF | 8co6_validation.cif.gz | 393.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/8co6 ftp://data.pdbj.org/pub/pdb/validation_reports/co/8co6 | HTTPS FTP |
-Related structure data
Related structure data | 16772MC 8bp8C 8coaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 86767.953 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A0A1Q2TSK9 #2: Protein | Mass: 37230.664 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A0A1Q2TSM6 #3: Protein | Mass: 44910.738 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A2T3S6 #4: Protein | Mass: 102412.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A2T3R1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Rotavirus A / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Rotavirus A |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Virus shell | Diameter: 1000 nm / Triangulation number (T number): 13 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 2.2 e/Å2 / Avg electron dose per subtomogram: 90 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1961 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 85 / Num. of volumes extracted: 1961 | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Atomic model building | Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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