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- EMDB-27823: Cryo-EM structure of Rous sarcoma virus strand transfer complex -
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Open data
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Basic information
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Title | Cryo-EM structure of Rous sarcoma virus strand transfer complex | |||||||||
![]() | Flipped map | |||||||||
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![]() | intasome / integrase-viral DNA complex / strand transfer complex / VIRAL PROTEIN-DNA complex | |||||||||
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 / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...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 / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
![]() | Pandey KK / Bera S / Shi K / Aihara H / Grandgenett DP | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration. Authors: Sibes Bera / Ke Shi / Hideki Aihara / Duane P Grandgenett / Krishan K Pandey / ![]() Abstract: Integration of retroviral DNA into the host genome involves the formation of integrase (IN)-DNA complexes termed intasomes. Further characterization of these complexes is needed to understand their ...Integration of retroviral DNA into the host genome involves the formation of integrase (IN)-DNA complexes termed intasomes. Further characterization of these complexes is needed to understand their assembly process. Here, we report the single-particle cryo-EM structure of the Rous sarcoma virus (RSV) strand transfer complex (STC) intasome produced with IN and a preassembled viral/target DNA substrate at 3.36 Å resolution. The conserved intasome core region consisting of IN subunits contributing active sites interacting with viral/target DNA has a resolution of 3 Å. Our structure demonstrated the flexibility of the distal IN subunits relative to the IN subunits in the conserved intasome core, similar to results previously shown with the RSV octameric cleaved synaptic complex intasome produced with IN and viral DNA only. An extensive analysis of higher resolution STC structure helped in the identification of nucleoprotein interactions important for intasome assembly. Using structure-function studies, we determined the mechanisms of several IN-DNA interactions critical for assembly of both RSV intasomes. We determined the role of IN residues R244, Y246, and S124 in cleaved synaptic complex and STC intasome assemblies and their catalytic activities, demonstrating differential effects. Taken together, these studies advance our understanding of different RSV intasome structures and molecular determinants involved in their assembly. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 66.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
Images | ![]() | 76.6 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 120.1 MB 120.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e14MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Flipped map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_27823_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_27823_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RSV strand transfer complex
Entire | Name: RSV strand transfer complex |
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Components |
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-Supramolecule #1: RSV strand transfer complex
Supramolecule | Name: RSV strand transfer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 257 KDa |
-Macromolecule #1: integrase
Macromolecule | Name: integrase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.926582 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: PLREAKDLHT ALHIGPRALS KACNISMQQA REVVQTCPHC NSAPALEAGV NPRGLGPLQI WQTDFTLEPR MAPRSWLAVT VDTASSAIV VTQHGRVTSV AVQHHWATAI AVLGRPKAIK TDNGSCFTSK STREWLARWG IAHTTGIPGN SQGQAMVERA N RLLKDKIR ...String: PLREAKDLHT ALHIGPRALS KACNISMQQA REVVQTCPHC NSAPALEAGV NPRGLGPLQI WQTDFTLEPR MAPRSWLAVT VDTASSAIV VTQHGRVTSV AVQHHWATAI AVLGRPKAIK TDNGSCFTSK STREWLARWG IAHTTGIPGN SQGQAMVERA N RLLKDKIR VLAEGDGFMK RIPTSKQGEL LAKAMYALNH FERGENTKTP IQKHWRPTVL TEGPPVKIRI ETGEWEKGWN VL VWGRGYA AVKNRDTDKV IWVPSRKVKP DITQKDEVTK K UniProtKB: Gag-Pol polyprotein |
-Macromolecule #2: DNA (42-MER)
Macromolecule | Name: DNA (42-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.047456 KDa |
Sequence | String: (DG)(DA)(DG)(DT)(DA)(DT)(DT)(DG)(DC)(DA) (DT)(DA)(DA)(DG)(DA)(DC)(DA)(DA)(DC)(DA) (DG)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA) (DA)(DG)(DA)(DA)(DG)(DA)(DA)(DG)(DA)(DC) (DA) (DC)(DT) |
-Macromolecule #3: DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*...
Macromolecule | Name: DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*AP*CP*TP*C)-3') type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.716363 KDa |
Sequence | String: (DA)(DA)(DT)(DG)(DT)(DT)(DG)(DT)(DC)(DT) (DT)(DA)(DT)(DG)(DC)(DA)(DA)(DT)(DA)(DC) (DT)(DC) |
-Macromolecule #4: DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*TP*CP*TP*TP*CP*TP*TP*TP*C)-3')
Macromolecule | Name: DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*TP*CP*TP*TP*CP*TP*TP*TP*C)-3') type: dna / ID: 4 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.821123 KDa |
Sequence | String: (DA)(DG)(DT)(DG)(DT)(DC)(DT)(DT)(DC)(DT) (DT)(DC)(DT)(DT)(DT)(DC) |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3000 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |