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- PDB-8puf: Structure of immature HTLV-1 CA-NTD from in vitro assembled MA126... -

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Basic information

Entry
Database: PDB / ID: 8puf
TitleStructure of immature HTLV-1 CA-NTD from in vitro assembled MA126-CANC tubes: axis angle 20 degrees
ComponentsGag protein (Fragment)
KeywordsVIRAL PROTEIN / Retrovirus / HTLV / immature capsid / CA / CA-NTD
Function / homology
Function and homology information


viral process / viral capsid / nucleic acid binding / zinc ion binding
Similarity search - Function
gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / 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: 6.1 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

Downloads & links

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Assembly

Deposited unit
A: Gag protein (Fragment)
B: Gag protein (Fragment)
C: Gag protein (Fragment)


Theoretical massNumber of molelcules
Total (without water)41,9093
Polymers41,9093
Non-polymers00
Water0
1


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

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Components

#1: Protein Gag protein (Fragment)


Mass: 13969.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5GX59

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 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: Escherichia coli (E. coli) / Strain: BL21 (DE3)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethaneTRIS1
250 mMsodium chlorideNaClSodium chloride1
30.5 mMtris(2-carboxyethyl)phosphineTCEP1
41 mMethylenediamintetraacetic acidEDTAEthylenediaminetetraacetic acid1
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: 95 % / Chamber temperature: 283 K / Details: Grids coated with 2nm continuous carbon layer

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Alignment procedure: COMA FREE / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: FEI TITAN KRIOS / Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDNominal defocus max (nm)Nominal defocus min (nm)Nominal magnification (X)
14000100080000
235001500105000
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Avg electron dose per subtomogram (e/Å2)Film or detector modelDetector mode
110.36753.5143.5GATAN K3 BIOQUANTUM (6k x 4k)
221.053.5143.5GATAN K2 QUANTUM (4k x 4k)COUNTING
EM imaging optics
Energyfilter nameIDImaging-IDEnergyfilter slit width (eV)
GIF Bioquantum1120
GIF Quantum LS2220
Image scans
WidthHeightIDImage recording-IDEntry-ID
57604092118PUF
37083838228PUF

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Processing

EM software
IDNameVersionCategoryImaging-IDDetails
1subTOMvolume selection
2Warp1.0.9volume selection
3MATLABR2018bvolume selection
4SerialEMimage acquisition1
6Warp1.0.9CTF correction
9UCSF Chimeramodel fitting
12SerialEMimage acquisition2
13CTFFIND4.1.10CTF correction
14NOVACTFCTF correction
18Warp1.0.9final Euler assignmentMultiparticle refinement in M
21RELION3.1.33D reconstruction
Image processingDetails: Datasets (1) and (2) combined during Multiparticle refinement. See Materials and methods for details.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7700 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionNum. of tomograms: 69 / Num. of volumes extracted: 245000
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingChain residue range: 13-125
Details: rigid body fit derived from refined model deposited in D_1292131146
Source name: Other / Type: other

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