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- EMDB-17929: Structure of immature HTLV-1 CA-NTD from in vitro assembled MA126... -

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Basic information

Entry
Database: EMDB / ID: EMD-17929
TitleStructure of immature HTLV-1 CA-NTD from in vitro assembled MA126-CANC tubes: pooled class
Map dataHTLV-1 CA-NTD lattice: B-factor sharpened map
Sample
  • Virus: Human T-cell leukemia virus type I
    • Protein or peptide: Gag protein (Fragment)
KeywordsRetrovirus / HTLV / immature capsid / CA / CA-NTD / VIRAL PROTEIN
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
Methodsubtomogram averaging / cryo EM / Resolution: 3.4 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: 2024
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-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17929.png

Downloads & links

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Map

FileDownload / File: emd_17929.map.gz / Format: CCP4 / Size: 55.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHTLV-1 CA-NTD lattice: B-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 244 pix.
= 323.788 Å		1.33 Å/pix.
x 244 pix.
= 323.788 Å		1.33 Å/pix.
x 244 pix.
= 323.788 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.327 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.6
Minimum - Maximum-7.60575 - 11.567745
Average (Standard dev.)0.03742537 (±0.4698491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions244244244
Spacing244244244
CellA=B=C: 323.788 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17929_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HTLV-1 CA-NTD lattice: Halfmap 2

Fileemd_17929_half_map_1.map
AnnotationHTLV-1 CA-NTD lattice: Halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HTLV-1 CA-NTD lattice: Halfmap 1

Fileemd_17929_half_map_2.map
AnnotationHTLV-1 CA-NTD lattice: 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 protein (Fragment)

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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: No / Virus empty: Yes

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Macromolecule #1: Gag protein (Fragment)

MacromoleculeName: Gag protein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human T-cell leukemia virus type I
Molecular weightTheoretical: 13.969809 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PVMHPHGAPP NHRPWQMKDL QAIKQEVSQA APGSPQFMQT IRLAVQQFDP TAKDLQDLLQ YLCSSLVASL HHQQLDSLIS EAETRGITG YNPLAGPLRV QANNPQQQGL RREYQQLWLA AFAALP

UniProtKB: Gag protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTRIStris(hydroxymethyl)aminomethane
50.0 mMNaClsodium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
1.0 mMEDTAethylenediamintetraacetic acid
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AMYLAMINE
VitrificationCryogen 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 ID1
MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingImage 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 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: 1.0 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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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingImage 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 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: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
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

Image recording ID1
DetailsDatasets (1) and (2) combined during Multiparticle refinement. See Materials and methods for details.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number subtomograms used: 134000
ExtractionNumber tomograms: 69 / Number images used: 245000
Software: (Name: subTOM, Warp (ver. 1.0.9), MATLAB (ver. R2018b))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1qrj

source_name: PDB, initial_model_type: experimental model

1g03

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8pu6:
Structure of immature HTLV-1 CA-NTD from in vitro assembled MA126-CANC tubes: pooled class

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