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Yorodumi- EMDB-20689: CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20689 | |||||||||
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Title | CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome | |||||||||
Map data | HIV-1 cleaved synaptic complex (CSC) intasome | |||||||||
Sample |
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Keywords | site-specific recombination / retrovirus / integrase / integration / nucleoprotein complex / TRANSFERASE-TRANSFERASE INHIBITOR-DNA complex | |||||||||
Function / homology | Function and homology information HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.67 Å | |||||||||
Authors | Li M / Chen X | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Mol Biol / Year: 2020 Title: A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies. Authors: Min Li / Xuemin Chen / Huaibin Wang / Kellie A Jurado / Alan N Engelman / Robert Craigie / Abstract: The low solubility and aggregation properties of HIV-1 integrase (IN) are major obstacles for biochemical and structural studies. The lens epithelium-derived growth factor (LEDGF) is a cellular ...The low solubility and aggregation properties of HIV-1 integrase (IN) are major obstacles for biochemical and structural studies. The lens epithelium-derived growth factor (LEDGF) is a cellular factor that binds IN and tethers preintegration complexes to chromatin before integration. The LEDGF also stimulates HIV-1 IN DNA strand transfer activity and improves its solubility in vitro. We show that these properties are conferred by a short peptide spanning residues 178 to 197 of the LEDGF that encompasses its AT-hook DNA-binding elements. The peptide stimulates HIV-1 IN activity both in trans and in cis. Fusion of the peptide to either the N- or C-terminus of IN results in maximal stimulation of concerted integration activity and greatly improves the solubility of the protein and nucleoprotein complexes of IN with viral DNA ends (intasomes). High-resolution structures of HIV-1 intasomes are required to understand the mechanism of IN strand transfer inhibitors (INSTIs), which are front-line drugs for the treatment of HIV-1, and how the virus can develop resistance to INSTIs. We have previously determined the structure of the HIV-1 strand transfer complex intasome. The improved biophysical properties of intasomes assembled with LEDGF peptide fusion IN have enabled us to determine the structure of the cleaved synaptic complex intasome, which is the direct target of INSTIs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20689.map.gz | 165.6 MB | EMDB map data format | |
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Header (meta data) | emd-20689-v30.xml emd-20689.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_20689.png | 79.9 KB | ||
Filedesc metadata | emd-20689.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20689 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20689 | HTTPS FTP |
-Validation report
Summary document | emd_20689_validation.pdf.gz | 520.2 KB | Display | EMDB validaton report |
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Full document | emd_20689_full_validation.pdf.gz | 519.8 KB | Display | |
Data in XML | emd_20689_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_20689_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20689 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20689 | HTTPS FTP |
-Related structure data
Related structure data | 6u8qMC 6vdkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20689.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV-1 cleaved synaptic complex (CSC) intasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HIV-1 CSC intasome
Entire | Name: HIV-1 CSC intasome |
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Components |
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-Supramolecule #1: HIV-1 CSC intasome
Supramolecule | Name: HIV-1 CSC intasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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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: 12 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 39.898355 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 AGIKQEFGIP YNPQSQGVIE SMNKELKKII GQ VRDQAEH LKTAVQMAVF IHNFKRKGGI GGYSAGERIV DIIATDIQTK ELQKQITKIQ NFRVYYRDSR DPVWKGPAKL LWK GEGAVV IQDNSDIKVV PRRKAKIIRD YGKQMAGDDC VASRQDED UniProtKB: Integrase |
-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: Escherichia coli (E. coli) |
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: Escherichia coli (E. coli) |
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: (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: 5 / 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
Buffer | pH: 6.2 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134763 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: COMMON LINE |