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- EMDB-17929: Structure of immature HTLV-1 CA-NTD from in vitro assembled MA126... -
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Open data
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Basic information
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Title | Structure of immature HTLV-1 CA-NTD from in vitro assembled MA126-CANC tubes: pooled class | |||||||||||||||
![]() | HTLV-1 CA-NTD lattice: B-factor sharpened map | |||||||||||||||
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![]() | Retrovirus / HTLV / immature capsid / CA / CA-NTD / VIRAL PROTEIN | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.4 Å | |||||||||||||||
![]() | Obr M / Percipalle M / Chernikova D / Yang H / Thader A / Pinke G / Porley D / Mansky LM / Dick RA / Schur FKM | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 | ![]() | 51.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.8 KB 26.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.7 KB | Display | ![]() |
Images | ![]() | 239.2 KB | ||
Masks | ![]() | 55.4 MB | ![]() | |
Others | ![]() ![]() | 41.6 MB 41.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pu6MC ![]() 8pu7C ![]() 8pu8C ![]() 8pu9C ![]() 8puaC ![]() 8pubC ![]() 8pucC ![]() 8pudC ![]() 8pueC ![]() 8pufC ![]() 8pugC ![]() 8puhC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | HTLV-1 CA-NTD lattice: B-factor sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.327 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: HTLV-1 CA-NTD lattice: Halfmap 2
File | emd_17929_half_map_1.map | ||||||||||||
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Annotation | HTLV-1 CA-NTD lattice: Halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HTLV-1 CA-NTD lattice: Halfmap 1
File | emd_17929_half_map_2.map | ||||||||||||
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Annotation | HTLV-1 CA-NTD lattice: Halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human T-cell leukemia virus type I
Entire | Name: ![]() |
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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: all / 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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-Macromolecule #1: Gag protein (Fragment)
Macromolecule | Name: Gag protein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.969809 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: PVMHPHGAPP NHRPWQMKDL QAIKQEVSQA APGSPQFMQT IRLAVQQFDP TAKDLQDLLQ YLCSSLVASL HHQQLDSLIS EAETRGITG YNPLAGPLRV QANNPQQQGL RREYQQLWLA AFAALP UniProtKB: Gag protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | helical array |
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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. |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.3675 sec. / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Image recording ID: 2 / 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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL | ||||||
Output model | ![]() PDB-8pu6: |