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Yorodumi- PDB-5m3j: Influenza B polymerase bound to four heptad repeats of serine 5 p... -
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-Basic information
Entry | Database: PDB / ID: 5m3j | ||||||
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Title | Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD | ||||||
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Keywords | VIRAL PROTEIN / influenza B virus 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 / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / 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 / mRNA Splicing - Minor Pathway / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / host cell mitochondrion / RNA polymerase II activity / 7-methylguanosine mRNA capping / 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 / Inhibition of DNA recombination at telomere / RNA Polymerase II Pre-transcription Events / cap snatching / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription termination / kinase binding / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / virion component / 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 / endonuclease activity / Estrogen-dependent gene expression / host cell cytoplasm / transcription by RNA polymerase II / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding / ubiquitin protein ligase binding / host cell nucleus / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Influenza B virus Homo Sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 | 5m3j.cif.gz | 937.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3j.ent.gz | 778 KB | Display | PDB format |
PDBx/mmJSON format | 5m3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m3j_validation.pdf.gz | 491.8 KB | Display | wwPDB validaton report |
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Full document | 5m3j_full_validation.pdf.gz | 500 KB | Display | |
Data in XML | 5m3j_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 5m3j_validation.cif.gz | 96.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3j ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3j | HTTPS FTP |
-Related structure data
Related structure data | 5m3hC 4wsaS 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: 85822.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag C-terminal linker and TEV site / Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Z9 |
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#2: Protein | Mass: 86207.016 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 B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase |
#3: Protein | Mass: 90844.109 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 B virus / Strain: B/Memphis/13/2003 / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3 |
-RNA chain , 2 types, 2 molecules RV
#4: RNA chain | Mass: 4321.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3' end vRNA promoter / Source: (synth.) Influenza B virus |
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#5: RNA chain | Mass: 4557.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' end vRNA promoter / Source: (synth.) Influenza B virus |
-Protein/peptide , 1 types, 1 molecules X
#6: Protein/peptide | Mass: 3216.893 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Four heptad repeats of serine 5 phosphorylated Pol II CTD Source: (synth.) Homo Sapiens (human) References: UniProt: P24928*PLUS, DNA-directed RNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.27 Å3/Da / Density % sol: 76.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD ...Details: FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD peptide. Reservoir solution contained 0.1 M bicine pH 9.0, 10% MPD. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 73405 / % possible obs: 99.9 % / Redundancy: 8.54 % / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Net I/σ(I): 8.38 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 8.63 % / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 1.02 / CC1/2: 0.547 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WSA Resolution: 3.5→49.07 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→49.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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