+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17938 | |||||||||||||||
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Title | Cryo-electron tomogram of HTLV-1 MA126CANC tubes | |||||||||||||||
Map data | cryo-electron tomogram containing HTLV-1 MA126CANC tubes | |||||||||||||||
Sample |
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Keywords | Retrovirus / HTLV / immature capsid / CA / VIRAL PROTEIN | |||||||||||||||
Biological species | Human T-cell leukemia virus type I | |||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||
Authors | Obr 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
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17938.map.gz | 109.5 MB | EMDB map data format | |
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Header (meta data) | emd-17938-v30.xml emd-17938.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_17938.png | 231.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17938 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17938 | HTTPS FTP |
-Validation report
Summary document | emd_17938_validation.pdf.gz | 581.6 KB | Display | EMDB validaton report |
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Full document | emd_17938_full_validation.pdf.gz | 581.1 KB | Display | |
Data in XML | emd_17938_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_17938_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17938 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17938 | HTTPS FTP |
-Related structure data
Related structure data | 8pu6C 8pu7C 8pu8C 8pu9C 8puaC 8pubC 8pucC 8pudC 8pueC 8pufC 8pugC 8puhC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17938.map.gz / Format: CCP4 / Size: 127.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | cryo-electron tomogram containing HTLV-1 MA126CANC tubes | ||||||||||||||||||||
Voxel size | X=Y=Z: 10.616 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human T-cell leukemia virus type I
Entire | Name: Human T-cell leukemia virus type I |
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Components |
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-Supramolecule #1: Human T-cell leukemia virus type I
Supramolecule | Name: 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
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AMYLAMINE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP / Details: Grids coated with 2nm continuous carbon layer. | |||||||||||||||
Sectioning | Other: NO SECTIONING | |||||||||||||||
Fiducial marker | Manufacturer: Aurion / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: 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 model | PDB ID: Chain - Residue range: 13-125 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: CA numbering of residues |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |