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- PDB-8puh: Structure of the immature HTLV-1 CA lattice from full-length Gag ... -

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Basic information

Entry
Database: PDB / ID: 8puh
TitleStructure of the immature HTLV-1 CA lattice from full-length Gag VLPs: CA-CTD refinement
ComponentsGag polyproteinGroup-specific antigen
KeywordsVIRAL 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
Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman T-cell leukemia virus type I
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.2 Å
AuthorsObr, 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
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)95,1062
Polymers95,1062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Gag polyprotein / Group-specific antigen / Pr53Gag


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Human T-cell leukemia virus type I / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human T-cell leukemia virus type I
Source (recombinant)Organism: Homo sapiens (human) / Strain: 293T / Cell: Human Embryonic Kidney
Details of virusEmpty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4 / Details: Phosphate-buffered saline (PBS) 1X
Buffer component
IDConc.NameFormulaBuffer-ID
1155.2 mMSodium ChlorideNaClSodium chloride1
22.7 mMSodium Phosphate dibasicNa2HPO4-7H2O1
31.5 mMPotassium Phosphate monobasicKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1subTOMvolume selection
2Warp1.0.9volume selection
3MATLABR2018bvolume selection
4SerialEMimage acquisition
6Warp1.0.9CTF correction
7CTFFIND4.1.10CTF correction
8NOVACTFCTF correction
11UCSF Chimeramodel fitting
15Warp1.0.9final Euler assignmentMultiparticle refinement in M
16RELION3.0.8classification
17Warp1.0.93D reconstructionRefinement and reconstruction in M
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 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 selectionNum. of tomograms: 85 / Num. of volumes extracted: 132000
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingChain residue range: 13-125 / Details: rigid body fit using AlphaFold derived model / Source name: AlphaFold / Type: in silico model

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