+Open data
-Basic information
Entry | Database: PDB / ID: 8qe5 | ||||||
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Title | Apo Hantaan virus polymerase in monomeric state | ||||||
Components | RNA-directed RNA polymerase L | ||||||
Keywords | VIRAL PROTEIN / Bunyavirus / Hantaan virus / polymerase / dimer | ||||||
Function / homology | Function and homology information RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / endonuclease activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | Hantaan virus 76-118 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Durieux Trouilleton, Q. / Arragain, B. / Malet, H. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural characterization of the oligomerization of full-length Hantaan virus polymerase into symmetric dimers and hexamers. Authors: Quentin Durieux Trouilleton / Dominique Housset / Paco Tarillon / Benoît Arragain / Hélène Malet / Abstract: Hantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete ...Hantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete cryo-electron microscopy structure of Hantaan virus polymerase in several oligomeric forms. Apo polymerase protomers can adopt two drastically different conformations, which assemble into two distinct symmetric homodimers, that can themselves gather to form hexamers. Polymerase dimerization induces the stabilization of most polymerase domains, including the C-terminal domain that contributes the most to dimer's interface, along with a lariat region that participates to the polymerase steadying. Binding to viral RNA induces significant conformational changes resulting in symmetric oligomer disruption and polymerase activation, suggesting the possible involvement of apo multimers as protecting systems that would stabilize the otherwise flexible C-terminal domains. Overall, these results provide insights into the multimerization capability of Hantavirus polymerase and may help to define antiviral compounds to counteract these life-threatening viruses. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qe5.cif.gz | 293.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qe5.ent.gz | 220 KB | Display | PDB format |
PDBx/mmJSON format | 8qe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qe5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8qe5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8qe5_validation.xml.gz | 51.8 KB | Display | |
Data in CIF | 8qe5_validation.cif.gz | 77.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/8qe5 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/8qe5 | HTTPS FTP |
-Related structure data
Related structure data | 18343MC 8qgtC 8qguC 8qh3C 8qhdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15151/ESRF-ES-1251041225 / Data set type: other data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 249476.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hantaan virus 76-118 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P23456 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hantaan virus polymerase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.25 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Hantaan virus 76-118 | ||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 25 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 77 K / Details: blot force 1 3s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.45 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14650 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3354153 | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1209529 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 19.56 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8C4S Pdb chain-ID: A / Accession code: 8C4S / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||
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