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Yorodumi- PDB-5m3h: Bat influenza A/H17N10 polymerase bound to four heptad repeats of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m3h | ||||||
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Title | Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD | ||||||
Components |
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Keywords | TRANSFERASE / influenza RNA-dependent RNA polymerase / vRNA promoter / Pol II serine 5 phosphorylated CTD peptide | ||||||
Function / homology | Function and homology information microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Formation of the Early Elongation Complex ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / cap snatching / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / 7-methylguanosine mRNA capping / viral transcription / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / host cell mitochondrion / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / virion component / promoter-specific chromatin binding / DNA-templated transcription termination / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / host cell cytoplasm / transcription by RNA polymerase II / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / ubiquitin protein ligase binding / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Influenza A virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lukarska, M. / Pflug, A. / Cusack, S. | ||||||
Funding support | France, 1items
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Citation | Journal: Nature / Year: 2017 Title: Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Authors: Lukarska, M. / Fournier, G. / Pflug, A. / Resa-Infante, P. / Reich, S. / Naffakh, N. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m3h.cif.gz | 484.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3h.ent.gz | 380.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3h ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3h | HTTPS FTP |
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-Related structure data
Related structure data | 5m3jC 4wsbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 84241.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal linker and TEV site / Source: (gene. exp.) Influenza A virus / Gene: PA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM92 |
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#2: Protein | Mass: 87936.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal linker and TEV site / Source: (gene. exp.) Influenza A virus / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase |
#3: Protein | Mass: 90168.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal linker, C-terminal linker and STREP tag and TEV site Source: (gene. exp.) Influenza A virus / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90 |
-RNA chain , 2 types, 2 molecules RV
#4: RNA chain | Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3 prime end of influenza vRNA promoter / Source: (synth.) Influenza A virus |
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#5: RNA chain | Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5 prime end of influenza vRNA promoter / Source: (synth.) Influenza A virus |
-Protein/peptide , 1 types, 2 molecules XY
#6: Protein/peptide | Mass: 3216.893 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic peptide corresponding to 4 heptad repeats of serine 5 phosphorylated Pol II CTD Source: (synth.) Homo sapiens (human) / References: UniProt: P24928*PLUS |
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-Non-polymers , 3 types, 266 molecules
#7: Chemical | ChemComp-ZN / | ||
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#8: Chemical | ChemComp-PO4 / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Bat influenza polymerase at 10 mgs per ml in 50 mM HEPES NaOH, 500 mM NaCl, 5% (v/v) glycerol, 2 mM TCEP at pH 7.5 with 1:1 ratio of vRNA promoter and CTD peptide mixed with 0.7-1.5 M ...Details: Bat influenza polymerase at 10 mgs per ml in 50 mM HEPES NaOH, 500 mM NaCl, 5% (v/v) glycerol, 2 mM TCEP at pH 7.5 with 1:1 ratio of vRNA promoter and CTD peptide mixed with 0.7-1.5 M sodium/potassium phosphate at pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 117997 / % possible obs: 99.6 % / Redundancy: 5.84 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.45 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.21 / CC1/2: 0.562 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WSB Resolution: 2.5→49.528 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.528 Å
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Refine LS restraints |
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LS refinement shell |
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