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- PDB-6qbt: Structure of the HTLV-2 integrase catalytic core domain in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qbt | ||||||
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Title | Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium (trimeric form) | ||||||
![]() | HTLV-2 integrase catalytic core domain | ||||||
![]() | TRANSFERASE / retrovirus / deltaretrovirus / integration / strand-transfer / nucleotidyltransferase | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / structural molecule activity / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barski, M.S. / Minnell, J.J. / Maertens, G.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56γ. Authors: Michał S Barski / Jordan J Minnell / Zuzana Hodakova / Valerie E Pye / Andrea Nans / Peter Cherepanov / Goedele N Maertens / ![]() Abstract: Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor ...Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor disease, unless a therapy becomes available. A key step in the establishment of infection is the integration of viral genetic material into the host genome, catalysed by the retroviral integrase (IN) enzyme. Here, we use X-ray crystallography and single-particle cryo-electron microscopy to determine the structure of the functional deltaretroviral IN assembled on viral DNA ends and bound to the B56γ subunit of its human host factor, protein phosphatase 2 A. The structure reveals a tetrameric IN assembly bound to two molecules of the phosphatase via a conserved short linear motif. Insight into the deltaretroviral intasome and its interaction with the host will be crucial for understanding the pattern of integration events in infected individuals and therefore bears important clinical implications. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 45.9 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qbvC ![]() 6qbwC ![]() 6tjuC ![]() 6toqC ![]() 7pelC ![]() 5cz1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19178.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 67.6 % Description: Elongated rods reaching up to 0.5 mm in length. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 14% PEG 8000, 100 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→40.98 Å / Num. obs: 12518 / % possible obs: 99.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1194 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CZ1 Resolution: 2.29→40.98 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 2.29→40.98 Å
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