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- PDB-6voy: Cryo-EM structure of HTLV-1 instasome -

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Basic information

Entry
Database: PDB / ID: 6voy
TitleCryo-EM structure of HTLV-1 instasome
Components
  • (DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)- ...) x 2
  • DNA (25-MER)
  • DNA-binding protein 7d
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
KeywordsDNA BINDING PROTEIN/DNA / Integrase / Intasome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein phosphatase type 2A complex / meiotic sister chromatid cohesion / 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 ...protein phosphatase type 2A complex / meiotic sister chromatid cohesion / 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 / Co-stimulation by CD28 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Co-inhibition by CTLA4 / Platelet sensitization by LDL / 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 / RNA endonuclease activity / Resolution of Sister Chromatid Cohesion / DNA damage response, signal transduction by p53 class mediator / RHO GTPases Activate Formins / RAF activation / Degradation of beta-catenin by the destruction complex / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Negative regulation of MAPK pathway / Separation of Sister Chromatids / 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 / symbiont entry into host cell / Golgi apparatus / signal transduction / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Integrase Zinc binding domain / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Armadillo-like helical / Alpha Horseshoe / Ribonuclease H superfamily / Armadillo-type fold / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Pol protein / DNA-binding protein 7d / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
Human T-cell leukemia virus type I
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBhatt, V. / Shi, K. / Sundborger, A. / Aihara, H.
Funding support United States, 1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: DNA-binding protein 7d
B: DNA-binding protein 7d
C: DNA-binding protein 7d
D: DNA-binding protein 7d
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
F: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
I: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
J: DNA (25-MER)
K: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
L: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
M: DNA (25-MER)
N: DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,41418
Polymers313,10412
Non-polymers3106
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
DNA-binding protein 7d / 7 kDa DNA-binding protein d / Sso7d


Mass: 43652.680 Da / Num. of mol.: 4 / Mutation: W24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea), (gene. exp.) Human T-cell leukemia virus type I
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: sso7d, sso7d-1, SSO10610, pol / Production host: Escherichia coli (E. coli) / References: UniProt: P39476, UniProt: A0A1Y1CAW1
#2: Protein Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61- ...PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61-gamma / PP2A B subunit isoform R5-gamma / Renal carcinoma antigen NY-REN-29


Mass: 40357.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13362

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DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)- ... , 2 types, 4 molecules ILKN

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


Mass: 15074.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3')


Mass: 6199.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human T-cell leukemia virus type I

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DNA chain , 1 types, 2 molecules JM

#4: DNA chain DNA (25-MER)


Mass: 7614.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human T-cell leukemia virus type I

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Non-polymers , 2 types, 6 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HTLV1 intasome / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Human T-cell leukemia virus type I
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18_3861refinement
PHENIX1.18_3861refinement
EM software
IDNameVersionCategory
8PHENIXmodel refinement
13RELION3.083D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30434 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 189.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.012618386
ELECTRON MICROSCOPYf_angle_d1.520825768
ELECTRON MICROSCOPYf_chiral_restr0.09992882
ELECTRON MICROSCOPYf_plane_restr0.01262630
ELECTRON MICROSCOPYf_dihedral_angle_d29.65196970

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