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Open data
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Basic information
Entry | Database: PDB / ID: 6tu5 | ||||||
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Title | Influenza A/H7N9 polymerase core (apo) | ||||||
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![]() | VIRAL PROTEIN / RNA-dependent RNA polymerase | ||||||
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 / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...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 / 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 / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cusack, S. / Pflug, A. | ||||||
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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 554.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.5 KB | Display | ![]() |
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Full document | ![]() | 517.9 KB | Display | |
Data in XML | ![]() | 84.9 KB | Display | |
Data in CIF | ![]() | 113.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6szuC ![]() 6szvC ![]() 6t0nC ![]() 6t0rC ![]() 6t0sC ![]() 6t0uC ![]() 6t0vC ![]() 6t0wC ![]() 6t2cC ![]() 6tw1C ![]() 4wsbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
#1: Protein | Mass: 59383.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal truncation deletes endonuclease Source: (gene. exp.) ![]() Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PA / Variant: H7N9 / Production host: ![]() References: UniProt: M9TI86, Hydrolases; Acting on ester bonds #2: Protein | Mass: 86496.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB1 / Variant: H7N9 / Production host: ![]() #3: Protein | Mass: 16203.751 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal sequence GSGSENLYFQ is linker and residual TEV cleavage site after cleavage Source: (gene. exp.) ![]() Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB2 / Variant: H7N9 / Production host: ![]() #4: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.01 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein at about 9 mg/ml 0.1 M Tris pH 7.0, 8-13% PEG 8K, 0.2 M MgCl2, 0.1 M guanidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 3.325→132.024 Å / Num. obs: 50439 / % possible obs: 92.7 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.057 / Rrim(I) all: 0.199 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.325→3.463 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.298 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2523 / CC1/2: 0.5 / Rrim(I) all: 2.388 / % possible all: 42.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WSB Resolution: 3.325→132.024 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 32.599 / SU ML: 0.499 / Cross valid method: FREE R-VALUE / ESU R Free: 0.617 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.623 Å2
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Refinement step | Cycle: LAST / Resolution: 3.325→132.024 Å
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Refine LS restraints |
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LS refinement shell |
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