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Yorodumi- PDB-8puh: Structure of the immature HTLV-1 CA lattice from full-length Gag ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8puh | |||||||||||||||
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Title | Structure of the immature HTLV-1 CA lattice from full-length Gag VLPs: CA-CTD refinement | |||||||||||||||
Components | Gag polyprotein | |||||||||||||||
Keywords | VIRAL PROTEIN / Retrovirus / HTLV / immature capsid / CA | |||||||||||||||
Function / homology | Function and homology information viral process / viral nucleocapsid / nucleic acid binding / structural molecule activity / zinc ion binding Similarity search - Function | |||||||||||||||
Biological species | Human T-cell leukemia virus type I | |||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.2 Å | |||||||||||||||
Authors | Obr, M. / Percipalle, M. / Chernikova, D. / Yang, H. / Thader, A. / Pinke, G. / Porley, D. / Mansky, L.M. / Dick, R.A. / Schur, F.K.M. | |||||||||||||||
Funding support | Austria, United States, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8puh.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8puh.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 8puh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8puh_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8puh_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8puh_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 8puh_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/8puh ftp://data.pdbj.org/pub/pdb/validation_reports/pu/8puh | HTTPS FTP |
-Related structure data
Related structure data | 17943MC 8pu6C 8pu7C 8pu8C 8pu9C 8puaC 8pubC 8pucC 8pudC 8pueC 8pufC 8pugC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 47553.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: gag / Cell line (production host): HEK / Production host: Homo sapiens (human) / Strain (production host): 293T / References: UniProt: P03345 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Human T-cell leukemia virus type I / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Human T-cell leukemia virus type I | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Strain: 293T / Cell: Human Embryonic Kidney | ||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: Phosphate-buffered saline (PBS) 1X | ||||||||||||||||||||
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 mesh size: 300 divisions/in. / Grid type: C-flat-2/2 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 80000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.32 sec. / Electron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 143.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 85 / Num. of volumes extracted: 132000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Chain residue range: 13-125 / Details: rigid body fit using AlphaFold derived model / Source name: AlphaFold / Type: in silico model |