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- PDB-6kur: Structure of influenza D virus polymerase bound to vRNA promoter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kur | |||||||||
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Title | Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B1) | |||||||||
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![]() | VIRAL PROTEIN/RNA / influenza D virus / polymerase / cryo-EM / VIRAL PROTEIN-RNA complex | |||||||||
Function / homology | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Peng, Q. / Peng, R. / Qi, J. / Gao, G.F. / Shi, Y. | |||||||||
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![]() | ![]() Title: Structural insight into RNA synthesis by influenza D polymerase. Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / ...Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / George F Gao / Yi Shi / ![]() Abstract: The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the ...The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design. #1: ![]() Title: Structural insight into RNA synthesis by influenza D polymerase. Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / ...Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / George F Gao / Yi Shi / ![]() Abstract: The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the ...The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 301.6 KB | Display | ![]() |
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PDB format | ![]() | 229.1 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 779.5 KB | Display | ![]() |
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Full document | ![]() | 792.3 KB | Display | |
Data in XML | ![]() | 46.3 KB | Display | |
Data in CIF | ![]() | 71.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9581MC ![]() 9577C ![]() 9578C ![]() 9579C ![]() 9580C ![]() 9582C ![]() 9887C ![]() 9888C ![]() 6kujC ![]() 6kukC ![]() 6kupC ![]() 6kutC ![]() 6kuuC ![]() 6kuvC ![]() 6kv5C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 83036.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: D/swine/Oklahoma/1334/2011 / Gene: P3 Production host: ![]() References: UniProt: K9LHJ4 |
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#2: Protein | Mass: 86138.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: D/swine/Oklahoma/1334/2011 / Gene: PB1 Production host: ![]() References: UniProt: K9LH03, RNA-directed RNA polymerase |
#3: Protein | Mass: 88480.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: D/swine/Oklahoma/1334/2011 / Gene: PB2 Production host: ![]() References: UniProt: K9LHF3 |
#4: RNA chain | Mass: 4337.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: RNA chain | Mass: 4918.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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: Structure of influenza D virus polymerase bound to vRNA promoter in mode B conformation (class B1) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | 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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 298468 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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