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- EMDB-17938: Cryo-electron tomogram of HTLV-1 MA126CANC tubes -

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Basic information

Entry
Database: EMDB / ID: EMD-17938
TitleCryo-electron tomogram of HTLV-1 MA126CANC tubes
Map datacryo-electron tomogram containing HTLV-1 MA126CANC tubes
Sample
  • Virus: Human T-cell leukemia virus type I
KeywordsRetrovirus / HTLV / immature capsid / CA / VIRAL PROTEIN
Biological speciesHuman T-cell leukemia virus type I
Methodelectron tomography / cryo EM
AuthorsObr M / Percipalle M / Chernikova D / Yang H / Thader A / Pinke G / Porley D / Mansky LM / Dick RA / Schur FKM
Funding support Austria, United States, 4 items
OrganizationGrant numberCountry
Austrian Science FundP31445 Austria
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 GM151775 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 DE032878 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147890 United States
CitationJournal: bioRxiv / Year: 2023
Title: Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice.
Authors: Martin Obr / Mathias Percipalle / Darya Chernikova / Huixin Yang / Andreas Thader / Gergely Pinke / Dario Porley / Louis M Mansky / Robert A Dick / Florian Km Schur /
Abstract: Human T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here ...Human T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here we report the results of cryo-electron tomography (cryo-ET) studies of HTLV-1 virus-like particles (VLPs) assembled , as well as derived from cells. This work shows that HTLV-1 employs an unconventional mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature CA tubular arrays reveals that the primary stabilizing component in HTLV-1 is CA-NTD. Mutagenesis and biophysical analysis support this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the CA-CTD. These results are the first to provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus, and this helps explain why HTLV-1 particles are morphologically distinct.
History
DepositionJul 17, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17938.png

Downloads & links

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Map

FileDownload / File: emd_17938.map.gz / Format: CCP4 / Size: 127.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-electron tomogram containing HTLV-1 MA126CANC tubes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.62 Å/pix.
x 150 pix.
= 1592.4 Å		10.62 Å/pix.
x 464 pix.
= 4925.824 Å		10.62 Å/pix.
x 480 pix.
= 5095.68 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.616 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-122.817819999999998 - 288.241460000000018
Average (Standard dev.)88.631195000000005 (±23.068338000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin8-8-44
Dimensions464480150
Spacing480464150
CellA: 5095.68 Å / B: 4925.824 Å / C: 1592.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human T-cell leukemia virus type I

EntireName: Human T-cell leukemia virus type I
Components
  • Virus: Human T-cell leukemia virus type I

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Supramolecule #1: Human T-cell leukemia virus type I

SupramoleculeName: Human T-cell leukemia virus type I / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11908 / Sci species name: Human T-cell leukemia virus type I / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statehelical array

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTRIStris(hydroxymethyl)aminomethane
50.0 mMNaClSodium chloridesodium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
1.0 mMEDTAEthylenediaminetetraacetic acidethylenediamintetraacetic acid
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AMYLAMINE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP / Details: Grids coated with 2nm continuous carbon layer.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Average exposure time: 1.05 sec. / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9.10) / Details: Weighted back projection with SIRT-like filter / Number images used: 41

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Atomic model buiding 1

Initial modelPDB ID:

1qrj


Chain - Residue range: 13-125 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: CA numbering of residues
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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