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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6202 | |||||||||
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Title | Electron cryo-microscopy of an RNA polymerase | |||||||||
![]() | Reconstruction of dimeric Influenza Virus RNA Polymerase | |||||||||
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![]() | Influenza RdRP / single particle reconstitution / replication | |||||||||
Function / homology | ![]() viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription ...viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding / host cell nucleus / RNA binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Chang S / Sun DP / Liang H / Wang J / Li J / Guo L / Wang X / Guan C / Boruah BM / Yuan L ...Chang S / Sun DP / Liang H / Wang J / Li J / Guo L / Wang X / Guan C / Boruah BM / Yuan L / Feng F / Yang M / Wojdyla J / Wang M / Wang HW / Liu Y | |||||||||
![]() | ![]() Title: Cryo-EM structure of influenza virus RNA polymerase complex at 4.3 Å resolution. Authors: Shenghai Chang / Dapeng Sun / Huanhuan Liang / Jia Wang / Jun Li / Lu Guo / Xiangli Wang / Chengcheng Guan / Bhargavi M Boruah / Lingmin Yuan / Feng Feng / Mingrui Yang / Lulan Wang / Yao ...Authors: Shenghai Chang / Dapeng Sun / Huanhuan Liang / Jia Wang / Jun Li / Lu Guo / Xiangli Wang / Chengcheng Guan / Bhargavi M Boruah / Lingmin Yuan / Feng Feng / Mingrui Yang / Lulan Wang / Yao Wang / Justyna Wojdyla / Lanjuan Li / Jiawei Wang / Meitian Wang / Genhong Cheng / Hong-Wei Wang / Yingfang Liu / ![]() ![]() Abstract: Replication and transcription of influenza virus genome mainly depend on its RNA-dependent RNA polymerase (RdRP), composed of the PA, PB1, and PB2 subunits. Although extensively studied, the ...Replication and transcription of influenza virus genome mainly depend on its RNA-dependent RNA polymerase (RdRP), composed of the PA, PB1, and PB2 subunits. Although extensively studied, the underlying mechanism of the RdRP complex is still unclear. Here we report the biochemical characterization of influenza RdRP subcomplex comprising PA, PB1, and N terminus of PB2, which exist as dimer in solution and can assemble into a tetramer state, regulated by vRNA promoter. Using single-particle cryo-electron microscopy, we have reconstructed the RdRP tetramer complex at 4.3 Å, highlighting the assembly and interfaces between monomers within the tetrameric structure. The individual RdRP subcomplex contains all the characterized motifs and appears as a cage-like structure. High-throughput mutagenesis profiling revealed that residues involved in the oligomer state formation are critical for viral life cycle. Our results lay a solid base for understanding the mechanism of replication of influenza and other negative-stranded RNA viruses. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9 KB | Display | ![]() |
Images | ![]() | 166.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 335.8 KB | Display | ![]() |
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Full document | ![]() | 335.4 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j9bMC ![]() 6203C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of dimeric Influenza Virus RNA Polymerase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : dimeric Influenza Virus RNA Polymerase
Entire | Name: dimeric Influenza Virus RNA Polymerase |
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Components |
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-Supramolecule #1000: dimeric Influenza Virus RNA Polymerase
Supramolecule | Name: dimeric Influenza Virus RNA Polymerase / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: Influenza Virus RNA Polymerase Complex
Macromolecule | Name: Influenza Virus RNA Polymerase Complex / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.8 / Details: 25 mM HEPES 200 mM NaCl and 1 mM EDTA |
Grid | Details: Quantifoil Cu R2/1 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: The grids were blotted for 6.5 s with 100% humidity and flash frozen in liquid ethane cooled at liquid nitrogen temperature using an FEI Vitrobot. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Oct 2, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 50 e/Å2 Details: Each image was fractionated into 32 sub-frames, with 0.25 s exposure time per frame. All dose-fractionated cryo-EM images were recorded using a semi-automated low-dose acquisition program UCSF-Image4 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 67066 |
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FSC plot (resolution estimation) | ![]() |