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Yorodumi- PDB-7z1z: MVV strand transfer complex (STC) intasome in complex with LEDGF/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z1z | |||||||||
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Title | MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Intasome / Integrase / MVV / Lentivirus / HIV / strand transfer complex / LEDGF / IBD / DNA / integration | |||||||||
Function / homology | Function and homology information dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / exoribonuclease H / euchromatin / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / viral capsid / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to heat / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / DNA-directed DNA polymerase / transcription coactivator activity / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont entry into host cell / chromatin binding / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Visna/maedi virus EV1 KV1772 Homo sapiens (human) DNA molecule (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Pye, V.E. / Ballandras-Colas, A. / Cherepanov, P. | |||||||||
Funding support | United Kingdom, United States, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Multivalent interactions essential for lentiviral integrase function. Authors: Ballandras-Colas, A. / Chivukula, V. / Gruszka, D.T. / Shan, Z. / Singh, P.K. / Pye, V.E. / McLean, R.K. / Bedwell, G.J. / Li, W. / Nans, A. / Cook, N.J. / Fadel, H.J. / Poeschla, E.M. / ...Authors: Ballandras-Colas, A. / Chivukula, V. / Gruszka, D.T. / Shan, Z. / Singh, P.K. / Pye, V.E. / McLean, R.K. / Bedwell, G.J. / Li, W. / Nans, A. / Cook, N.J. / Fadel, H.J. / Poeschla, E.M. / Griffiths, D.J. / Vargas, J. / Taylor, I.A. / Lyumkis, D. / Yardimci, H. / Engelman, A.N. / Cherepanov, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z1z.cif.gz | 772 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z1z.ent.gz | 638.4 KB | Display | PDB format |
PDBx/mmJSON format | 7z1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z1z_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7z1z_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7z1z_validation.xml.gz | 117 KB | Display | |
Data in CIF | 7z1z_validation.cif.gz | 176.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/7z1z ftp://data.pdbj.org/pub/pdb/validation_reports/z1/7z1z | HTTPS FTP |
-Related structure data
Related structure data | 14453MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 18 molecules ABCDEFGHIJKLMNOPRQ
#1: Protein | Mass: 32368.826 Da / Num. of mol.: 16 / Fragment: UNP residues 821-1101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Visna/maedi virus EV1 KV1772 / Strain: KV1772 / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: P35956, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, dUTP diphosphatase, ...References: UniProt: P35956, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, dUTP diphosphatase, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds #2: Protein | Mass: 11075.970 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O75475 |
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-DNA chain , 3 types, 6 molecules XYWZUa
#3: DNA chain | Mass: 7064.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #4: DNA chain | Mass: 15387.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #5: DNA chain | Mass: 7073.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
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-Non-polymers , 1 types, 12 molecules
#6: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MVV STC intasome in complex with LEDGF / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 0.48 MDa / Experimental value: NO |
Source (natural) | Organism: Visna/maedi virus EV1 KV1772 |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6.5 Details: 310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5. |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The intasomes were typically assembled by incubating 7 uM MVV IN, 8 uM LEDGF/p75, and 3.75 uM annealed vDNA (or the strand transfer product mimic) in 80 mM NaCl, 40 mM potassium acetate, 3 ...Details: The intasomes were typically assembled by incubating 7 uM MVV IN, 8 uM LEDGF/p75, and 3.75 uM annealed vDNA (or the strand transfer product mimic) in 80 mM NaCl, 40 mM potassium acetate, 3 mM CaCl2 10 uM ZnCl2, 1 mM dithiothreitol (DTT) and 25 mM BisTris-HCl, pH 6.0 in a total volume of 200 ul at 37 deg C for 10 min (to prepare samples for cryo-EM, the reaction was upscaled to a total volume of 1 ml). The opalescent mixture was supplemented with 50 mM BisTris-HCl, pH 6.5 and 190 mM NaCl and incubated on ice for 5 min to clear. If starting volume exceeded 200 ul, the mixture was concentrated by ultrafiltration in a VivaSpin device to a final volume of 200 ul. Intasomes were purified by size exclusion chromatography through a Superdex-200 10/30 column (GE Healthcare) pre-equilibrated in 310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5. |
Specimen support | Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 36232 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
Software | Name: PHENIX / Version: dev_4213: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121619 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: interactive fitting/rebuilding in coot and real space refinement in Phenix. | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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