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- PDB-8r65: 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8r65 | ||||||||||||||||||||||||
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Title | 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide with ordered PB2 C-terminal domains | ||||||||||||||||||||||||
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![]() | VIRAL PROTEIN / influenza / polymerase / PolII-CTD | ||||||||||||||||||||||||
Function / homology | ![]() cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.23 Å | ||||||||||||||||||||||||
![]() | Keown, J.R. / Carrique, L. / Fodor, E. / Grimes, J.M. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide with ordered PB2 C-terminal domains Authors: Keown, J.R. / Carrique, L. / Fodor, E. / Grimes, J.M. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 745.6 KB | Display | ![]() |
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PDB format | ![]() | 614.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 73.5 KB | Display | |
Data in CIF | ![]() | 109.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18947MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules ACB
#1: Protein | Mass: 82663.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PA / Production host: ![]() ![]() |
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#2: Protein | Mass: 102377.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PB2 / Production host: ![]() ![]() |
#6: Protein | Mass: 86625.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PB1 / Production host: ![]() ![]() |
-RNA chain , 2 types, 2 molecules DE
#3: RNA chain | Mass: 4862.017 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
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#4: RNA chain | Mass: 5335.125 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
-Protein/peptide , 1 types, 1 molecules X
#5: Protein/peptide | Mass: 3216.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide with ordered PB2 C-terminal domains Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16121 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT Details: The model from 8R60 was used as a starting point. The PB2 C-terminal domains (7NHX) were split into Cap-binding domain and 627/NLS domains which were rigid body fit into the density. ...Details: The model from 8R60 was used as a starting point. The PB2 C-terminal domains (7NHX) were split into Cap-binding domain and 627/NLS domains which were rigid body fit into the density. Seperate models were manually linked |
Atomic model building | PDB-ID: 7NHX Accession code: 7NHX / Source name: PDB / Type: experimental model |