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- EMDB-4709: The structure of a Ty3 retrotransposon icosahedral capsid -

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Entry
Database: EMDB / ID: EMD-4709
TitleThe structure of a Ty3 retrotransposon icosahedral capsid
Map data
SampleT9 icosahedral capsid of a Ty3 retrotransposon:
Transposon Ty3-I Gag-Pol polyprotein
Function / homology
Function and homology information


retrotransposon nucleocapsid / transposition, RNA-mediated / Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases / ribonuclease H / ribonuclease activity / RNA-directed DNA polymerase / DNA integration / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity ...retrotransposon nucleocapsid / transposition, RNA-mediated / Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases / ribonuclease H / ribonuclease activity / RNA-directed DNA polymerase / DNA integration / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / RNA binding / DNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm
Integrase core domain / Ribonuclease H-like superfamily / Integrase, catalytic core / Zinc finger, CCHC-type / Ty3 transposon peptidase / Zinc finger CCHC-type profile. / Reverse transcriptase (RT) catalytic domain profile. / Integrase catalytic domain profile. / Aspartic peptidase domain superfamily / Peptidase A2B, Ty3 transposon peptidase ...Integrase core domain / Ribonuclease H-like superfamily / Integrase, catalytic core / Zinc finger, CCHC-type / Ty3 transposon peptidase / Zinc finger CCHC-type profile. / Reverse transcriptase (RT) catalytic domain profile. / Integrase catalytic domain profile. / Aspartic peptidase domain superfamily / Peptidase A2B, Ty3 transposon peptidase / Ribonuclease H superfamily / Zinc finger, CCHC-type superfamily / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain
Transposon Ty3-I Gag-Pol polyprotein
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsDodonova SO / Prinz S / Bilanchone V / Sandmeyer S / Briggs JAG
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.
Validation ReportPDB-ID: 6r24

SummaryFull reportAbout validation report
DateDeposition: Mar 15, 2019 / Header (metadata) release: May 31, 2017 / Map release: May 8, 2019 / Update: May 22, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6r24
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6r24
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4709.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 600 pix.
= 648. Å
1.08 Å/pix.
x 600 pix.
= 648. Å
1.08 Å/pix.
x 600 pix.
= 648. 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
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.022254843 - 0.040721588
Average (Standard dev.)0.0007404633 (±0.0048266537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z648.000648.000648.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0220.0410.001

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Supplemental data

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Sample components

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Entire T9 icosahedral capsid of a Ty3 retrotransposon

EntireName: T9 icosahedral capsid of a Ty3 retrotransposon
Details: The asymmetric unit contains 9 monomers of the Ty3 capsid molecule.
Number of components: 2

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Component #1: protein, T9 icosahedral capsid of a Ty3 retrotransposon

ProteinName: T9 icosahedral capsid of a Ty3 retrotransposon
Details: The asymmetric unit contains 9 monomers of the Ty3 capsid molecule.
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: pJK776 / Strain: yVB1680 strain - BY4741 killer minus, Ty3 null

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Component #2: protein, Transposon Ty3-I Gag-Pol polyprotein

ProteinName: Transposon Ty3-I Gag-Pol polyprotein
Details: D336I mutation in the active center of the Ty3 protease
Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 36.382371 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 296 K / Humidity: 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
ImagingMicroscope: 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 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 gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1236
3D reconstructionSoftware: RELION / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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