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Yorodumi- PDB-8r1j: Structure of avian H5N1 influenza A polymerase dimer in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r1j | |||||||||||||||||||||
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Title | Structure of avian H5N1 influenza A polymerase dimer in complex with human ANP32B. | |||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza virus / replication platform / H5N1 / influenza adaptive mutations / host adaptation / viral polymerase / cryo-EM / HPAI. | |||||||||||||||||||||
Function / homology | Function and homology information ventricular system development / vasculature development / RNA polymerase binding / roof of mouth development / cap snatching / viral transcription / inner ear development / negative regulation of cell differentiation / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / positive regulation of protein export from nucleus ...ventricular system development / vasculature development / RNA polymerase binding / roof of mouth development / cap snatching / viral transcription / inner ear development / negative regulation of cell differentiation / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / positive regulation of protein export from nucleus / : / nucleosome assembly / histone binding / endonuclease activity / regulation of apoptotic process / host cell cytoplasm / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / host cell nucleus / RNA binding / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Influenza A virus Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Carrique, L. / Staller, E. / Keown, J.R. / Fan, H. / Fodor, E. / Grimes, J.M. | |||||||||||||||||||||
Funding support | United Kingdom, 6items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation. Authors: Ecco Staller / Loïc Carrique / Olivia C Swann / Haitian Fan / Jeremy R Keown / Carol M Sheppard / Wendy S Barclay / Jonathan M Grimes / Ervin Fodor / Abstract: Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by ...Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by species-specific variation in acidic nuclear phosphoprotein 32 (ANP32) proteins, which are essential for viral RNA genome replication. Adaptive mutations enable the IAV RNA polymerase (FluPolA) to surmount this barrier. Here, we present cryo-electron microscopy structures of monomeric and dimeric avian H5N1 FluPolA with human ANP32B. ANP32B interacts with the PA subunit of FluPolA in the monomeric form, at the site used for its docking onto the C-terminal domain of host RNA polymerase II during viral transcription. ANP32B acts as a chaperone, guiding FluPolA towards a ribonucleoprotein-associated FluPolA to form an asymmetric dimer-the replication platform for the viral genome. These findings offer insights into the molecular mechanisms governing IAV genome replication, while enhancing our understanding of the molecular processes underpinning mammalian adaptations in avian-origin FluPolA. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r1j.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8r1j.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8r1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r1j_validation.pdf.gz | 945.6 KB | Display | wwPDB validaton report |
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Full document | 8r1j_full_validation.pdf.gz | 985.6 KB | Display | |
Data in XML | 8r1j_validation.xml.gz | 106.6 KB | Display | |
Data in CIF | 8r1j_validation.cif.gz | 161.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/8r1j ftp://data.pdbj.org/pub/pdb/validation_reports/r1/8r1j | HTTPS FTP |
-Related structure data
Related structure data | 18818MC 8r1lC 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 |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 82600.281 Da / Num. of mol.: 2 / Mutation: Q556R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/turkey/Turkey/1/2005(H5N1) / Gene: PA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A5Z236 #2: Protein | Mass: 86616.312 Da / Num. of mol.: 2 / Mutation: K577E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/turkey/Turkey/1/2005(H5N1) / Gene: PB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A5Z231, RNA-directed RNA polymerase #3: Protein | Mass: 101380.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/turkey/Turkey/1/2005(H5N1) / Gene: PB2 / Production host: Spodoptera frugiperda (fall armyworm) #4: Protein | | Mass: 28816.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANP32B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92688 |
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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: Structure of avian H5N1 influenza A polymerase dimer in complex with human ANP32B. Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||
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Molecular weight | Value: 0.55 MDa / Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Influenza A virus / Strain: A/turkey/Turkey/1/2005(H5N1) | ||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 24000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105000 / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1
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