+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43756 | |||||||||
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Title | HIV-1 P5-IN intasome core | |||||||||
Map data | Primary map | |||||||||
Sample |
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Keywords | HIV-1 / integrase / nucleoprotein complexes / INSTI / intasome / CryoEM / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Li M / Craigie R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Mol Biol / Year: 2024 Title: HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro. Authors: Min Li / Renbin Yang / Xuemin Chen / Huaibin Wang / Rodolfo Ghirlando / Emilios K Dimitriadis / Robert Craigie / Abstract: Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) in which a pair of viral DNA ends are bridged by a multimer of integrase (IN). Most of the high-resolution structures of ...Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) in which a pair of viral DNA ends are bridged by a multimer of integrase (IN). Most of the high-resolution structures of HIV-1 intasomes are based on an HIV-1 IN with an Sso7d protein domain fused to the N-terminus. Sso7d-IN aggregates much less than wild-type IN and has been critical for structural studies of HIV-1 intasomes. Unexpectedly, these structures revealed that the common core architecture that mediates catalysis could be assembled in various ways, giving rise to both tetrameric and dodecameric intasomes, together with other less well-characterized species. This differs from related retroviruses that assemble unique multimeric intasomes, although the number of protomers in the intasome varies between viruses. The question of whether the additional Sso7d domain contributes to the heterogeneity of HIV-1 intasomes is therefore raised. We have addressed this by biochemical and structural studies of intasomes assembled with wild-type HIV-1 IN. Negative stain and cryo-EM reveal a similar range of multimeric intasome species as with Sso7d-IN with the same common core architecture. Stacks of intasomes resulting from domain swapping are also seen with both wild-type and Sso7d-IN intasomes. The propensity to assemble multimeric intasome species is, therefore, an intrinsic property of HIV-1 IN and is not conferred by the presence of the Sso7d domain. The recently solved intasome structures of different retroviral species, which have been reported to be tetrameric, octameric, dodecameric, and hexadecameric, highlight how a common intasome core architecture can be assembled in different ways for catalysis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43756.map.gz | 139 MB | EMDB map data format | |
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Header (meta data) | emd-43756-v30.xml emd-43756.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43756_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_43756.png | 69.2 KB | ||
Filedesc metadata | emd-43756.cif.gz | 6.5 KB | ||
Others | emd_43756_additional_1.map.gz emd_43756_half_map_1.map.gz emd_43756_half_map_2.map.gz | 2.1 MB 139.7 MB 139.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43756 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43756 | HTTPS FTP |
-Related structure data
Related structure data | 8w2rMC 8w09C 8w34C 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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-Map
File | Download / File: emd_43756.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Primary map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_43756_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half1 map
File | emd_43756_half_map_1.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map
File | emd_43756_half_map_2.map | ||||||||||||
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Annotation | Half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 P5-IN intasomes Core
Entire | Name: HIV-1 P5-IN intasomes Core |
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Components |
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-Supramolecule #1: HIV-1 P5-IN intasomes Core
Supramolecule | Name: HIV-1 P5-IN intasomes Core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: HIV-1 intasomes assembled with P5-IN |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: Integrase
Macromolecule | Name: Integrase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 39.850418 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HMKKRGRPAA TEVKIKKKRG RPPLPAGTNS KGPPDFSSDE EREPTPVLGS GAAAAGQSRA AVGRKATKKT DGGGFLDGID KAQEEHEKY HSNWRAMASD FNLPPVVAKE IVASCDKCQL KGEAMHGQVD CSPGIWQLDC THLEGKVILV AVHVASGYIE A EVIPAETG ...String: HMKKRGRPAA TEVKIKKKRG RPPLPAGTNS KGPPDFSSDE EREPTPVLGS GAAAAGQSRA AVGRKATKKT DGGGFLDGID KAQEEHEKY HSNWRAMASD FNLPPVVAKE IVASCDKCQL KGEAMHGQVD CSPGIWQLDC THLEGKVILV AVHVASGYIE A EVIPAETG QETAYFLLKL AGRWPVKTVH TDNGSNFTST TVKAACWWAG IKQEFGIPYN PQSQGVIESM NKELKKIIGQ VR DQAEHLK TAVQMAVFIH NFKRKGGIGG YSAGERIVDI IATDIQTKEL QKQITKIQNF RVYYRDSRDP VWKGPAKLLW KGE GAVVIQ DNSDIKVVPR RKAKIIRDYG KQMAGDDCVA SRQDED UniProtKB: Integrase |
-Macromolecule #2: DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*...
Macromolecule | Name: DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*G)-3') type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
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 (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3') type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
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: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 6.2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |