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- EMDB-4708: The structure of a Ty3 retrotransposon capsid C-terminal domain dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-4708
TitleThe structure of a Ty3 retrotransposon capsid C-terminal domain dimer
Map dataThe structure of a Ty3 capsid C-terminal domain dimer
Sample
  • Complex: Ty3 capsid C-terminal domain dimer
    • Protein or peptide: Transposon Ty3-I Gag-Pol polyprotein
KeywordsTy3 / retrotransposon / retrovirus / capsid / Gag polyprotein / capsid-CTD / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / viral translational frameshifting / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Peptidase A2B, Ty3 transposon peptidase / Ty3 transposon peptidase / Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Integrase core domain ...Peptidase A2B, Ty3 transposon peptidase / Ty3 transposon peptidase / Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Transposon Ty3-I Gag-Pol polyprotein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsDodonova SO / Prinz S
Funding support Germany, United Kingdom, 2 items
OrganizationGrant numberCountry
German Research FoundationBR 3635/2-1 Germany
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
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
Header (metadata) releaseMay 31, 2017-
DepositionMar 15, 2019-
Map releaseMay 8, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r23
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4708.png

Downloads & links

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Map

FileDownload / File: emd_4708.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of a Ty3 capsid C-terminal domain dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 160 pix.
= 172.8 Å		1.08 Å/pix.
x 160 pix.
= 172.8 Å		1.08 Å/pix.
x 160 pix.
= 172.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-3.4644072 - 8.104494000000001
Average (Standard dev.)0.02595305 (±0.29507926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 172.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z172.800172.800172.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-3.4648.1040.026

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Supplemental data

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Sample components

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Entire : Ty3 capsid C-terminal domain dimer

EntireName: Ty3 capsid C-terminal domain dimer
Components
  • Complex: Ty3 capsid C-terminal domain dimer
    • Protein or peptide: Transposon Ty3-I Gag-Pol polyprotein

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Supramolecule #1: Ty3 capsid C-terminal domain dimer

SupramoleculeName: Ty3 capsid C-terminal domain dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The 9 non-symmetry related copies of the Ty3 Capsid-CTD from the complete capsid shell structure were aligned and averaged to generate a higher resolution 4.9 A structure
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Transposon Ty3-I Gag-Pol polyprotein

MacromoleculeName: Transposon Ty3-I Gag-Pol polyprotein / type: protein_or_peptide / ID: 1
Details: D336I mutation in the active center of the Ty3 protease
Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 36.382371 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND ASRIVYCRRH LLNPAAQWAN DFVQEQGIL EITFDTFIQG LYQHFYKPPD INKIFNAITQ LSEAKLGIER LNQRFRKIWD RMPPDFMTEK AAIMTYTRLL T KETYNIVR ...String:
MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND ASRIVYCRRH LLNPAAQWAN DFVQEQGIL EITFDTFIQG LYQHFYKPPD INKIFNAITQ LSEAKLGIER LNQRFRKIWD RMPPDFMTEK AAIMTYTRLL T KETYNIVR MHKPETLKDA MEEAYQTTAL TERFFPGFEL DADGDTIIGA TTHLQEEYDS DYDSEDNLTQ NRYVHTVRTR RS YNKPMSN HRNRRNNNAS REECIKNRLC FYCKKEGHRL NECRARKAVL TDLELESKDQ QTLFIKTLPI VH

UniProtKB: Transposon Ty3-I Gag-Pol polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationNameFormula
10.0 mMTris
100.0 mMNaCl
1.0 mMEDTA
GridModel: C-flat / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 296 K / Instrument: HOMEMADE PLUNGER
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

MicroscopeFEI TITAN KRIOS
DetailsCryo-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.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1727
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: TOM Toolbox
Details: The Ty3 particles have a T=9 and each asymmetric unit of the lattice contains nine non-symmetry related Ty3 capsid protein monomers. We extracted all non-symmetry related units from the ...Details: The Ty3 particles have a T=9 and each asymmetric unit of the lattice contains nine non-symmetry related Ty3 capsid protein monomers. We extracted all non-symmetry related units from the final reconstructions from the two half datasets. The CA-CTDs were aligned and averaged separately. The final structure of the CA-CTD comes from nine averaged copies of the domain. The final structure of the CA-CTD was resolved at 4.9 A resolution at 0.143 FSC. Gaussian-smoothened ellipsoid-shaped masks were used for resolution measurements.
Number images used: 74160
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6r23:
The structure of a Ty3 retrotransposon capsid C-terminal domain dimer

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