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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 dataIntasome
Sample
  • Complex: HTLV1 intasome
    • Protein or peptide: DNA-binding protein 7d
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
    • DNA: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
    • DNA: DNA (25-MER)
    • DNA: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsIntegrase / Intasome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein phosphatase type 2A complex / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated ...protein phosphatase type 2A complex / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Platelet sensitization by LDL / CTLA4 inhibitory signaling / protein phosphatase activator activity / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Resolution of Sister Chromatid Cohesion / RNA endonuclease activity / RHO GTPases Activate Formins / RAF activation / Degradation of beta-catenin by the destruction complex / DNA integration / RNA stem-loop binding / Negative regulation of MAPK pathway / Separation of Sister Chromatids / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Regulation of TP53 Degradation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA recombination / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of cell population proliferation / Golgi apparatus / signal transduction / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / DNA-binding 7kDa protein / 7kD DNA-binding domain / Chromo-like domain superfamily / Integrase Zinc binding domain / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / DNA-binding 7kDa protein / 7kD DNA-binding domain / Chromo-like domain superfamily / Integrase Zinc binding domain / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Armadillo-like helical / Armadillo-type fold / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Pol protein / DNA-binding protein 7d / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Similarity search - Component
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 / Heather O 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 / Heather O 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.
History
DepositionFeb 1, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseJul 1, 2020-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21301.png

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)
AnnotationIntasome
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00782 / Movie #1: 0.00782
Minimum - Maximum-0.03814228 - 0.06626419
Average (Standard dev.)0.0000066219186 (±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
Components
  • Complex: HTLV1 intasome
    • Protein or peptide: DNA-binding protein 7d
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
    • DNA: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
    • DNA: DNA (25-MER)
    • DNA: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: HTLV1 intasome

SupramoleculeName: HTLV1 intasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Human T-cell leukemia virus type I

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Macromolecule #1: DNA-binding protein 7d

MacromoleculeName: DNA-binding protein 7d / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human T-cell leukemia virus type I
Molecular weightTheoretical: 43.65268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MATVKFKYKG EEKEVDISKI KKVARVGKMI SFTYDEGGGK TGEGAVSEKD APKELLQMLE KQKKGGSLE VLFQGPSPAE LHSFTHCGQT ALTLQGATTT EASNILRSCH ACRKNNPQHQ MPRGHIRRGL LPNHIWQGDI T HFKYKNTL ...String:
MGSSHHHHHH SSGLVPRGSH MATVKFKYKG EEKEVDISKI KKVARVGKMI SFTYDEGGGK TGEGAVSEKD APKELLQMLE KQKKGGSLE VLFQGPSPAE LHSFTHCGQT ALTLQGATTT EASNILRSCH ACRKNNPQHQ MPRGHIRRGL LPNHIWQGDI T HFKYKNTL YRLHVWVDTF SGAISATQKR KETSSEAISS LLQAIAYLGK PSYINTDNGP AYISQDFLNM CTSLAIRHTT HV PYNPTSS GLVQRSNGIL KTLLYKYFTD KPDLPMDNAL SIALWTINHL NVLTNCHKTR WQLHHSPRLQ PIPETRSLSN KQT HWYYFK LPGLNSRQWK GPQEALQEAA GAALIPVSAS SAQWIPWRLL KRAACPRPVG GPADPKEKDH QHHG

UniProtKB: DNA-binding protein 7d, Pol protein

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Macromolecule #2: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.357789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IRDVPPADQE KLFIQKLRQC CVLFDFVSDP LSDLKWKEVK RAALSEMVEY ITHNRNVITE PIYPEVVHMF AVNMFRTLPP SSNPTGAEF DPEEDEPTLE AAWPHLQLVY EFFLRFLESP DFQPNIAKKY IDQKFVLQLL ELFDSEDPRE RDFLKTTLHR I YGKFLGLR ...String:
IRDVPPADQE KLFIQKLRQC CVLFDFVSDP LSDLKWKEVK RAALSEMVEY ITHNRNVITE PIYPEVVHMF AVNMFRTLPP SSNPTGAEF DPEEDEPTLE AAWPHLQLVY EFFLRFLESP DFQPNIAKKY IDQKFVLQLL ELFDSEDPRE RDFLKTTLHR I YGKFLGLR AYIRKQINNI FYRFIYETEH HNGIAELLEI LGSIINGFAL PLKEEHKIFL LKVLLPLHKV KSLSVYHPQL AY CVVQFLE KDSTLTEPVV MALLKYWPKT HSPKEVMFLN ELEEILDVIE PSEFVKIMEP LFRQLAKCVS SPHFQVAERA LYY WNNEYI MSLISDNAAK ILPIMFP

UniProtKB: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform

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Macromolecule #3: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')

MacromoleculeName: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.074711 KDa
SequenceString:
(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)

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Macromolecule #4: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Human T-cell leukemia virus type I
Molecular weightTheoretical: 7.614918 KDa
SequenceString:
(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)

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Macromolecule #5: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')

MacromoleculeName: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Human T-cell leukemia virus type I
Molecular weightTheoretical: 6.199017 KDa
SequenceString:
(DG)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DT)(DT) (DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DT)(DG)

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 30434
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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