+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14860 | |||||||||||||||
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Title | Cryo-EM structure of the MVV CSC intasome at 4.5A resolution | |||||||||||||||
Map data | deepEMnhancer map | |||||||||||||||
Sample |
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Function / homology | Function and homology information dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral capsid / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | |||||||||||||||
Biological species | Visna/maedi virus EV1 KV1772 / Visna-maedi virus / Visna lentivirus (strain 1514) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
Authors | Ballandras-Colas A / Maskell D / Pye VE / Locke J / Swuec S / Kotecha A / Costa A / Cherepanov P | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Science / Year: 2017 Title: A supramolecular assembly mediates lentiviral DNA integration. Authors: Allison Ballandras-Colas / Daniel P Maskell / Erik Serrao / Julia Locke / Paolo Swuec / Stefán R Jónsson / Abhay Kotecha / Nicola J Cook / Valerie E Pye / Ian A Taylor / Valgerdur ...Authors: Allison Ballandras-Colas / Daniel P Maskell / Erik Serrao / Julia Locke / Paolo Swuec / Stefán R Jónsson / Abhay Kotecha / Nicola J Cook / Valerie E Pye / Ian A Taylor / Valgerdur Andrésdóttir / Alan N Engelman / Alessandro Costa / Peter Cherepanov / Abstract: Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the ...Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 angstrom resolution. The intasome comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture featuring eight structurally distinct types of IN protomers supporting two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C-terminal domains from flanking tetramers completing the synaptic interface. Our results explain how HIV-1 IN, which self-associates into higher-order multimers, can form a functional intasome, reconcile the bulk of early HIV-1 IN biochemical and structural data, and provide a lentiviral platform for design of HIV-1 IN inhibitors. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14860.map.gz | 92.5 MB | EMDB map data format | |
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Header (meta data) | emd-14860-v30.xml emd-14860.xml | 27.2 KB 27.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14860_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_14860.png | 175.5 KB | ||
Masks | emd_14860_msk_1.map | 103 MB | Mask map | |
Others | emd_14860_additional_1.map.gz emd_14860_additional_2.map.gz emd_14860_half_map_1.map.gz emd_14860_half_map_2.map.gz | 51.2 MB 2.8 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14860 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14860 | HTTPS FTP |
-Related structure data
Related structure data | 7zppMC 4139C 5lljC 5m0rC 5t3aC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14860.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | deepEMnhancer map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.43 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14860_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: original map - no enhancement
File | emd_14860_additional_1.map | ||||||||||||
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Annotation | original map - no enhancement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: cryosparc local filter map - to which model...
File | emd_14860_additional_2.map | ||||||||||||
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Annotation | cryosparc local filter map - to which model was fitted and refined against | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_14860_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14860_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Maedi-visna virus (MVV) intasome
Entire | Name: Maedi-visna virus (MVV) intasome |
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Components |
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-Supramolecule #1: Maedi-visna virus (MVV) intasome
Supramolecule | Name: Maedi-visna virus (MVV) intasome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 542.45 KDa |
-Supramolecule #2: Intergrase
Supramolecule | Name: Intergrase / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Visna/maedi virus EV1 KV1772 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: vDNA
Supramolecule | Name: vDNA / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Visna-maedi virus |
-Macromolecule #1: Integrase
Macromolecule | Name: Integrase / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: Visna/maedi virus EV1 KV1772 / Strain: KV1772 |
Molecular weight | Theoretical: 32.368826 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: WIENIPLAEE EHNKWHQDAV SLHLEFGIPR TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE TNSGLIYAE RVKGETGQEF RVQTMKWYAM FAPKSLQSDN GPAFVAESTQ LLMKYLGIEH TTGIPWNPQS QALVERTHQT L KNTLEKLI ...String: WIENIPLAEE EHNKWHQDAV SLHLEFGIPR TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE TNSGLIYAE RVKGETGQEF RVQTMKWYAM FAPKSLQSDN GPAFVAESTQ LLMKYLGIEH TTGIPWNPQS QALVERTHQT L KNTLEKLI PMFNAFESAL AGTLITLNIK RKGGLGTSPM DIFIFNKEQQ RIQQQSKSKQ EKIRFCYYRT RKRGHPGEWQ GP TQVLWGG DGAIVVKDRG TDRYLVIANK DVKFIPPPKE IQKE |
-Macromolecule #2: vDNA, non-transferred strand
Macromolecule | Name: vDNA, non-transferred strand / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Visna lentivirus (strain 1514) |
Molecular weight | Theoretical: 6.456146 KDa |
Sequence | String: (DG)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DA)(DT) (DC)(DC)(DG)(DC)(DT)(DC)(DC)(DG)(DG)(DT) (DG) |
-Macromolecule #3: vDNA, transferred strand
Macromolecule | Name: vDNA, transferred strand / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Visna-maedi virus |
Molecular weight | Theoretical: 5.815762 KDa |
Sequence | String: (DC)(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG) (DG)(DA)(DT)(DC)(DT)(DC)(DG)(DC)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 6.5 Component:
Details: 1 M NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl, pH 6.5 | ||||||||||||
Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV Details: To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and ...Details: To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s followed by plunging into liquid ethane.. | ||||||||||||
Details | A 4 ul drop of freshly prepared intasome in 1 M NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 was applied onto glow-discharged lacey carbon grids coated with ultrathin carbon (product 01824, Ted Pella). The grids were incubated for 30 s under 100% humidity in a Vitrobot Mark IV (FEI) at 20 oC. To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4 ul drop of 200 mM NaCl, 3 mM CaCl2, and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s, followed by plunging into liquid ethane. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: 5m0q |
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Details | 5M0Q model was docked to new map (updated relion version and pixel size corrected) in Chimera and refined using phenix.real_space refine and interactively adjusted in coot. |
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 100 / Target criteria: correlation coefficient |
Output model | PDB-7zpp: |