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- PDB-6szu: Bat Influenza A polymerase pre-termination complex with pyrophosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6szu | ||||||
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Title | Bat Influenza A polymerase pre-termination complex with pyrophosphate using 44-mer vRNA template with mutated oligo(U) sequence | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wandzik, J.M. / Kouba, T. / Cusack, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase. Authors: Joanna M Wandzik / Tomas Kouba / Manikandan Karuppasamy / Alexander Pflug / Petra Drncova / Jan Provaznik / Nayara Azevedo / Stephen Cusack / ![]() ![]() Abstract: Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). ...Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory. After exiting the active site cavity, the template 3' extremity rebinds into a specific site on the polymerase surface. Here, it remains sequestered during all subsequent transcription steps, forcing the template to loop out as it further translocates. At termination, the strained connection between the bound template 5' end and the active site results in polyadenylation by stuttering at uridine 17. Upon product dissociation, further conformational changes release the trapped template, allowing recycling back into the pre-initiation state. Influenza polymerase thus performs transcription while tightly binding to and protecting both template ends, allowing efficient production of multiple mRNAs from a single vRNP. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 368.3 KB | Display | ![]() |
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PDB format | ![]() | 279.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10354MC ![]() 6szvC ![]() 6t0nC ![]() 6t0rC ![]() 6t0sC ![]() 6t0uC ![]() 6t0vC ![]() 6t0wC ![]() 6t2cC ![]() 6tu5C ![]() 6tw1C 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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1 |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 85490.930 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: 87936.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PB1 / Production host: ![]() ![]() ![]() |
#3: Protein | Mass: 91027.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PB2 / Production host: ![]() ![]() |
-RNA chain , 2 types, 2 molecules VM
#4: RNA chain | ![]() Mass: 14012.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#5: RNA chain | ![]() Mass: 3223.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 319 molecules ![](data/chem/img/M4H.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-M4H / | ||||
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#7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-POP / | ![]() #9: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
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: 39 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 257175 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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