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Open data
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Basic information
Entry | Database: PDB / ID: 6r24 | |||||||||
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Title | The structure of a Ty3 retrotransposon icosahedral capsid | |||||||||
![]() | Transposon Ty3-I Gag-Pol polyprotein | |||||||||
![]() | VIRUS LIKE PARTICLE / Ty3 / retrotransposon / retrovirus / capsid / Gag polyprotein | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
![]() | Dodonova, S.O. / Prinz, S. / Bilanchone, V. / Sandmeyer, S. / Briggs, J.A.G. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses. Authors: Svetlana O Dodonova / Simone Prinz / Virginia Bilanchone / Suzanne Sandmeyer / John A G Briggs / ![]() ![]() ![]() Abstract: Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR ...Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains of which can oligomerize to form a virus-like particle. The structures of retroviral capsids have been extensively described. They assemble an immature viral particle through oligomerization of full-length Gag. Proteolytic cleavage of Gag results in a mature, infectious particle. In contrast, the absence of structural data on LTR retrotransposon capsids hinders our understanding of their function and evolutionary relationships. Here, we report the capsid morphology and structure of the archetypal Gypsy retrotransposon Ty3. We performed electron tomography (ET) of immature and mature Ty3 particles within cells. We found that, in contrast to retroviruses, these do not change size or shape upon maturation. Cryo-ET and cryo-electron microscopy of purified, immature Ty3 particles revealed an irregular fullerene geometry previously described for mature retrovirus core particles and a tertiary and quaternary arrangement of the capsid (CA) C-terminal domain within the assembled capsid that is conserved with mature HIV-1. These findings provide a structural basis for studying retrotransposon capsids, including those domesticated in higher organisms. They suggest that assembly via a structurally distinct immature capsid is a later retroviral adaptation, while the structure of mature assembled capsids is conserved between LTR retrotransposons and retroviruses. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 200.4 KB | Display | ![]() |
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PDB format | ![]() | 116.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4709MC ![]() 4707C ![]() 4708C ![]() 6r22C ![]() 6r23C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 36382.371 Da / Num. of mol.: 9 / Mutation: D336I Source method: isolated from a genetically manipulated source Details: D336I mutation in the active center of the Ty3 protease Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TY3B-I, YILWTy3-1 POL, YIL082W-A / Plasmid: pJK776 / Production host: ![]() ![]() Strain (production host): yVB1680 strain - BY4741 killer minus, Ty3 null References: UniProt: Q7LHG5, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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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 |
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Sample preparation
Component | Name: T9 icosahedral capsid of a Ty3 retrotransposon / Type: COMPLEX Details: The asymmetric unit contains 9 monomers of the Ty3 capsid molecule. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Natural host | Organism: Saccharomyces cerevisiae | ||||||||||||||||||||
Virus shell | Name: GAG Capsid / Diameter: 480 nm / Triangulation number (T number): 9 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat | ||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 296 K Details: The sample was applied onto glow-discharged C-flat (Protochips Inc.) holey carbon grids. The grids were blotted from the back side for 11 seconds at room temperature in a chamber at 85% ...Details: The sample was applied onto glow-discharged C-flat (Protochips Inc.) holey carbon grids. The grids were blotted from the back side for 11 seconds at room temperature in a chamber at 85% humidity and plunge-frozen into liquid ethane using a manual plunger. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Cryo-grids containing purified PR- Ty3 particles were imaged in a Titan Krios electron microscope equipped with a Falcon II direct electron detector, operated at 300 kV. Images were ...Details: Cryo-grids containing purified PR- Ty3 particles were imaged in a Titan Krios electron microscope equipped with a Falcon II direct electron detector, operated at 300 kV. Images were collected with a nominal magnification of 75000, giving a pixel size of 1.08 A. Images were collected in integrating mode with a total electron dose of 20 e/A2. The range of applied defocus values was between -1.0 um and -3.5 um. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Movie frames/image: 1 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1727 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1236 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
EM volume selection | Details: 1733 vesicles and near-complete buds were picked from 61 tomograms. Subtomograms were extracted from the surface of the vesicles. Num. of tomograms: 54 / Num. of volumes extracted: 2547 | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient |