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- EMDB-17943: Structure of the immature HTLV-1 CA lattice from full-length Gag ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17943
TitleStructure of the immature HTLV-1 CA lattice from full-length Gag VLPs: CA-CTD refinement
Map dataHTLV-1 Gag-based VLPs, CA-CTD refinement, B-factor sharpened map
Sample
  • Virus: Human T-cell leukemia virus type I
    • Protein or peptide: Gag polyprotein
KeywordsRetrovirus / HTLV / immature capsid / CA / VIRAL PROTEIN
Function / homology
Function and homology information


viral nucleocapsid / nucleic acid binding / viral translational frameshifting / 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 ...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
Methodsubtomogram averaging / cryo EM / Resolution: 6.2 Å
AuthorsObr 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
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: Nat Struct Mol Biol / Year: 2025
Title: Distinct 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 K M Schur /
Abstract: Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron ...Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results 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, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17943.png

Downloads & links

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Map

FileDownload / File: emd_17943.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHTLV-1 Gag-based VLPs, CA-CTD refinement, B-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 320 pix.
= 441.92 Å		1.38 Å/pix.
x 320 pix.
= 441.92 Å		1.38 Å/pix.
x 320 pix.
= 441.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.381 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.014068392 - 0.021913823
Average (Standard dev.)0.00014205219 (±0.00078410195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 441.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: HTLV-1 Gag-based VLPs, CA-CTD refinement, denoised map

Fileemd_17943_additional_1.map
AnnotationHTLV-1 Gag-based VLPs, CA-CTD refinement, denoised map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HTLV-1 Gag-based VLPs, CA-CTD refinement, halfmap 2

Fileemd_17943_half_map_1.map
AnnotationHTLV-1 Gag-based VLPs, CA-CTD refinement, halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HTLV-1 Gag-based VLPs, CA-CTD refinement, halfmap 1

Fileemd_17943_half_map_2.map
AnnotationHTLV-1 Gag-based VLPs, CA-CTD refinement, halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human T-cell leukemia virus type I

EntireName: Human T-cell leukemia virus type I
Components
  • Virus: Human T-cell leukemia virus type I
    • Protein or peptide: Gag polyprotein

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Supramolecule #1: Human T-cell leukemia virus type I

SupramoleculeName: 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: Yes / Virus empty: Yes

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Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human T-cell leukemia virus type I
Molecular weightTheoretical: 47.553234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQIFSRSAS PIPRPPRGLA AHHWLNFLQA AYRLEPGPSS YDFHQLKKFL KIALETPARI CPINYSLLAS LLPKGYPGRV NEILHILIQ TQAQIPSRPA PPPPSSPTHD PPDSDPQIPP PYVEPTAPQV LPVMHPHGAP PNHRPWQMKD LQAIKQEVSQ A APGSPQFM ...String:
MGQIFSRSAS PIPRPPRGLA AHHWLNFLQA AYRLEPGPSS YDFHQLKKFL KIALETPARI CPINYSLLAS LLPKGYPGRV NEILHILIQ TQAQIPSRPA PPPPSSPTHD PPDSDPQIPP PYVEPTAPQV LPVMHPHGAP PNHRPWQMKD LQAIKQEVSQ A APGSPQFM QTIRLAVQQF DPTAKDLQDL LQYLCSSLVA SLHHQQLDSL ISEAETRGIT GYNPLAGPLR VQANNPQQQG LR REYQQLW LAAFAALPGS AKDPSWASIL QGLEEPYHAF VERLNIALDN GLPEGTPKDP ILRSLAYSNA NKECQKLLQA RGH TNSPLG DMLRACQTWT PKDKTKVLVV QPKKPPPNQP CFRCGKAGHW SRDCTQPRPP PGPCPLCQDP THWKRDCPRL KPTI PEPEP EEDALLLDLP ADIPHPKNSI GGEV

UniProtKB: Gag polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
155.2 mMNaClSodium Chloride
2.7 mMNa2HPO4-7H2OSodium Phosphate dibasic
1.5 mMKH2PO4Potassium Phosphate monobasic

Details: Phosphate-buffered saline (PBS) 1X
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.32 sec. / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 80000
Sample stageSpecimen 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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Software - details: Refinement and reconstruction in M / Number subtomograms used: 29000
ExtractionNumber tomograms: 85 / Number images used: 132000
Software: (Name: subTOM, Warp (ver. 1.0.9), MATLAB (ver. R2018b))
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Warp (ver. 1.0.9) / Software - details: Multiparticle refinement in M

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Atomic model buiding 1

Initial modelChain - Residue range: 13-125 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: rigid body fit using AlphaFold derived model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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