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- EMDB-29318: Structure of G140A/Q148K HIV-1 intasome with Dolutegravir bound -
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Open data
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Basic information
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Title | Structure of G140A/Q148K HIV-1 intasome with Dolutegravir bound | ||||||||||||||||||
![]() | Density modified and resampled map of G140A/Q148K HIV-1 intasome with drug Dolutegravir | ||||||||||||||||||
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![]() | Integrase / Nucleoprotein complex / Inhibitor / Drug resistance / VIRAL PROTEIN-DNA-INHIBITOR complex | ||||||||||||||||||
Function / homology | ![]() lamin binding / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...lamin binding / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / nuclear envelope / RNA-directed DNA polymerase activity / host cell / 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 / cadherin binding / symbiont entry into host cell / lipid binding / host cell nucleus / chromatin / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane / nucleus Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||
![]() | Shan ZL / Passos DO / Strutzenberg TS / Li M / Lyumkis D | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Authors: Min Li / Dario Oliveira Passos / Zelin Shan / Steven J Smith / Qinfang Sun / Avik Biswas / Indrani Choudhuri / Timothy S Strutzenberg / Allan Haldane / Nanjie Deng / Zhaoyang Li / Xue Zhi ...Authors: Min Li / Dario Oliveira Passos / Zelin Shan / Steven J Smith / Qinfang Sun / Avik Biswas / Indrani Choudhuri / Timothy S Strutzenberg / Allan Haldane / Nanjie Deng / Zhaoyang Li / Xue Zhi Zhao / Lorenzo Briganti / Mamuka Kvaratskhelia / Terrence R Burke / Ronald M Levy / Stephen H Hughes / Robert Craigie / Dmitry Lyumkis / ![]() Abstract: HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), ...HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26 KB 26 KB | Display Display | ![]() |
Images | ![]() | 172.7 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() ![]() | 108.1 MB 200.5 MB 200.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fnmMC ![]() 8fn7C ![]() 8fndC ![]() 8fngC ![]() 8fnhC ![]() 8fnjC ![]() 8fnlC ![]() 8fnnC ![]() 8fnoC ![]() 8fnpC ![]() 8fnqC C: citing same article ( M: atomic model generated by this map |
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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
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Annotation | Density modified and resampled map of G140A/Q148K HIV-1 intasome with drug Dolutegravir | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.38 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map of G140A/Q148K HIV-1 intasome with drug Dolutegravir
File | emd_29318_additional_1.map | ||||||||||||
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Annotation | Unsharpened map of G140A/Q148K HIV-1 intasome with drug Dolutegravir | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map2 of G140A/Q148K HIV-1 intasome with drug Dolutegravir
File | emd_29318_half_map_1.map | ||||||||||||
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Annotation | Half map2 of G140A/Q148K HIV-1 intasome with drug Dolutegravir | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map1 of G140A/Q148K HIV-1 intasome with drug Dolutegravir
File | emd_29318_half_map_2.map | ||||||||||||
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Annotation | Half map1 of G140A/Q148K HIV-1 intasome with drug Dolutegravir | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : G140A/Q148K HIV-1 intasome bound to dolutegravir
Entire | Name: G140A/Q148K HIV-1 intasome bound to dolutegravir |
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Components |
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-Supramolecule #1: G140A/Q148K HIV-1 intasome bound to dolutegravir
Supramolecule | Name: G140A/Q148K HIV-1 intasome bound to dolutegravir / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Lamina-associated polypeptide 2, isoform alpha,Integrase chimera
Macromolecule | Name: Lamina-associated polypeptide 2, isoform alpha,Integrase chimera type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.913434 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMPKRGRP AATEVKIPKP RGRPPLPAGT NSKGPPDFSS DEEREPTPVL GSGAAAAGQS RAAVGRKATK KTDGGGFLDG IDKAQEEHE KYHSNWRAMA SDFNLPPVVA KEIVASCDKC QLKGEAMHGQ VDCSPGIWQL DCTHLEGKVI LVAVHVASGY I EAEVIPAE ...String: GSHMPKRGRP AATEVKIPKP RGRPPLPAGT NSKGPPDFSS DEEREPTPVL GSGAAAAGQS RAAVGRKATK KTDGGGFLDG IDKAQEEHE KYHSNWRAMA SDFNLPPVVA KEIVASCDKC QLKGEAMHGQ VDCSPGIWQL DCTHLEGKVI LVAVHVASGY I EAEVIPAE TGQETAYFLL KLAGRWPVKT VHTDNGSNFT STTVKAACWW AGIKQEFAIP YNPQSKGVIE SMNKELKKII GQ VRDQAEH LKTAVQMAVF IHNFKRKGGI GGYSAGERIV DIIATDIQTK ELQKQITKIQ NFRVYYRDSR DPVWKGPAKL LWK GEGAVV IQDNSDIKVV PRRKAKIIRD YGKQMAGDDC VASRQDED UniProtKB: Lamina-associated polypeptide 2, isoform alpha, Gag-Pol polyprotein |
-Macromolecule #2: DNA (27-MER)
Macromolecule | Name: DNA (27-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.188271 KDa |
Sequence | String: (DA)(DC)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG) (DA)(DT)(DT)(DT)(DT)(DC)(DC)(DC)(DG)(DC) (DC)(DC)(DA)(DC)(DG)(DC)(DT) |
-Macromolecule #3: DNA (25-MER)
Macromolecule | Name: DNA (25-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.773023 KDa |
Sequence | String: (DA)(DG)(DC)(DG)(DT)(DG)(DG)(DG)(DC)(DG) (DG)(DG)(DA)(DA)(DA)(DA)(DT)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA) |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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 |
-Macromolecule #6: (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4...
Macromolecule | Name: (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide type: ligand / ID: 6 / Number of copies: 2 / Formula: DLU |
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Molecular weight | Theoretical: 419.379 Da |
Chemical component information | ![]() ChemComp-DLU: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 430 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 58139 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-8fnm: |