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- EMDB-21301: Cryo-EM structure of HTLV-1 instasome -

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Basic information

Entry
Database: EMDB / ID: EMD-21301
TitleCryo-EM structure of HTLV-1 instasome
Map data
SampleHTLV1 intasome
  • DNA-binding protein 7d
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
  • (nucleic-acidNucleic acid) x 3
  • (ligand) x 2
Function / homology
Function and homology information


regulation of protein autophosphorylation / protein phosphatase type 2A complex / protein phosphatase regulator activity / protein phosphatase activator activity / negative regulation of protein kinase B signaling / regulation of phosphatidylinositol 3-kinase signaling / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / endoribonuclease activity / protein dephosphorylation ...regulation of protein autophosphorylation / protein phosphatase type 2A complex / protein phosphatase regulator activity / protein phosphatase activator activity / negative regulation of protein kinase B signaling / regulation of phosphatidylinositol 3-kinase signaling / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / endoribonuclease activity / protein dephosphorylation / DNA integration / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / negative regulation of cell population proliferation / signal transduction / Golgi apparatus / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
DNA-binding 7kDa protein / Integrase, C-terminal, retroviral / Reverse transcriptase/Diguanylate cyclase domain / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Chromo-like domain superfamily / Armadillo-type fold / Ribonuclease H-like superfamily / Armadillo-like helical / Integrase, N-terminal zinc-binding domain ...DNA-binding 7kDa protein / Integrase, C-terminal, retroviral / Reverse transcriptase/Diguanylate cyclase domain / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Chromo-like domain superfamily / Armadillo-type fold / Ribonuclease H-like superfamily / Armadillo-like helical / Integrase, N-terminal zinc-binding domain / Reverse transcriptase domain / Protein phosphatase 2A, regulatory B subunit, B56 / Ribonuclease H domain / Integrase, catalytic core
Pol protein / DNA-binding protein 7d / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Biological speciesHuman T-cell leukemia virus type I / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBhatt V / Shi K / Sundborger A / Aihara H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of host protein hijacking in human T-cell leukemia virus integration.
Authors: Veer Bhatt / Ke Shi / Daniel J Salamango / Nicholas H Moeller / Krishan K Pandey / Sibes Bera / Thomas E Bohl / Fredy Kurniawan / Kayo Orellana / Wei Zhang / Duane P Grandgenett / Reuben S ...Authors: Veer Bhatt / Ke Shi / Daniel J Salamango / Nicholas H Moeller / Krishan K Pandey / Sibes Bera / Thomas E Bohl / Fredy Kurniawan / Kayo Orellana / Wei Zhang / Duane P Grandgenett / Reuben S Harris / Anna C Sundborger-Lunna / Hideki Aihara /
Abstract: Integration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses, including an oncogenic delta(δ)-retrovirus human T-cell leukemia virus ...Integration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses, including an oncogenic delta(δ)-retrovirus human T-cell leukemia virus type-1 (HTLV-1). Retroviral integrase forms a higher order nucleoprotein assembly (intasome) to catalyze the integration reaction, in which the roles of host factors remain poorly understood. Here, we use cryo-electron microscopy to visualize the HTLV-1 intasome at 3.7-Å resolution. The structure together with functional analyses reveal that the B56γ (B'γ) subunit of an essential host enzyme, protein phosphatase 2 A (PP2A), is repurposed as an integral component of the intasome to mediate HTLV-1 integration. Our studies reveal a key host-virus interaction underlying the replication of an important human pathogen and highlight divergent integration strategies of retroviruses.
Validation ReportPDB-ID: 6voy

SummaryFull reportAbout validation report
History
DepositionFeb 1, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00782
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00782
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6voy
  • Surface level: 0.00782
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21301.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 264 pix.
= 235.831 Å
0.89 Å/pix.
x 264 pix.
= 235.831 Å
0.89 Å/pix.
x 264 pix.
= 235.831 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8933 Å
Density
Contour LevelBy AUTHOR: 0.00782 / Movie #1: 0.00782
Minimum - Maximum-0.03814228 - 0.06626419
Average (Standard dev.)0.00000662192 (±0.0024679683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 235.83119 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.893299242424240.893299242424240.89329924242424
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z235.831235.831235.831
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.0380.0660.000

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Supplemental data

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Sample components

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Entire HTLV1 intasome

EntireName: HTLV1 intasome / Number of components: 8

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Component #1: protein, HTLV1 intasome

ProteinName: HTLV1 intasome / Recombinant expression: No
SourceSpecies: Human T-cell leukemia virus type I
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, DNA-binding protein 7d

ProteinName: DNA-binding protein 7d / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 43.65268 kDa
SourceSpecies: Human T-cell leukemia virus type I
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Serine/threonine-protein phosphatase 2A 56 kDa regulator...

ProteinName: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 40.357789 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*...

nucleic acidName: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DG)(DA) (DA)(DA)(DT)(DT)(DT)(DA)(DG)(DT)(DA)(DC) (DA)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DA) (DA)(DG)(DT)(DG)(DT)(DG)(DT)(DC)(DC)
MassTheoretical: 15.074711 kDa
SourceSpecies: Homo sapiens (human)

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Component #5: nucleic-acid, DNA (25-MER)

nucleic acidName: DNA (25-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DC)(DT)(DG)(DT)(DG)(DT)(DA)(DC)(DT) (DA)(DA)(DA)(DT)(DT)(DT)(DC)(DT)(DC)(DT) (DC)(DC)(DT)(DG)(DG)
MassTheoretical: 7.614918 kDa
SourceSpecies: Human T-cell leukemia virus type I

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Component #6: nucleic-acid, DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*...

nucleic acidName: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DT)(DT) (DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DT)(DG)
MassTheoretical: 6.199017 kDa
SourceSpecies: Human T-cell leukemia virus type I

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Component #7: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 30434
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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