+Open data
-Basic information
Entry | Database: PDB / ID: 6rwo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SIVrcm intasome (Q148H/G140S) in complex with bictegravir | |||||||||
Components |
| |||||||||
Keywords | RECOMBINATION / retroviral integrase / lentivirus / strand transfer inhibior / protein-DNA complex | |||||||||
Function / homology | Function and homology information exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Simian immunodeficiency virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Cherepanov, P. / Nans, A. / Cook, N. | |||||||||
Funding support | United States, United Kingdom, 2items
| |||||||||
Citation | Journal: Science / Year: 2020 Title: Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Authors: Nicola J Cook / Wen Li / Dénes Berta / Magd Badaoui / Allison Ballandras-Colas / Andrea Nans / Abhay Kotecha / Edina Rosta / Alan N Engelman / Peter Cherepanov / Abstract: Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We ...Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rwo.cif.gz | 426.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rwo.ent.gz | 337.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rwo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rwo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6rwo_validation.xml.gz | 70 KB | Display | |
Data in CIF | 6rwo_validation.cif.gz | 105.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/6rwo ftp://data.pdbj.org/pub/pdb/validation_reports/rw/6rwo | HTTPS FTP |
-Related structure data
Related structure data | 10044MC 6rwlC 6rwmC 6rwnC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 1 types, 12 molecules AENLKJIMFDCB
#1: Protein | Mass: 32772.223 Da / Num. of mol.: 12 / Mutation: Q148H, G140S, A119D Source method: isolated from a genetically manipulated source Details: SIVrcm integrase / Source: (gene. exp.) Simian immunodeficiency virus / Gene: pol / Variant: SIV of red-capped mangabeys / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): PC2 / References: UniProt: E1ANT8 |
---|
-DNA chain , 2 types, 4 molecules QSWT
#2: DNA chain | Mass: 10134.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Gene: U5 LTR end / Variant: SIV of red-capped mangabeys / Production host: synthetic construct (others) #3: DNA chain | Mass: 9223.995 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Gene: U5 LTR end / Variant: SIV of red-capped mangabeys / Production host: synthetic construct (others) |
---|
-Non-polymers , 5 types, 22 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MG / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6618 |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217635 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
|