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Yorodumi- EMDB-4423: Helical part of the influenza A virus ribonucleoprotein. Conforma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4423 | |||||||||
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Title | Helical part of the influenza A virus ribonucleoprotein. Conformation 3. | |||||||||
Map data | Inuenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation 3. | |||||||||
Sample |
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Function / homology | Function and homology information negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Influenza A virus (A/Wilson-Smith/1933(H1N1)) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Coloma R / Arranz R / de la Rosa-Trevin JM / Sorzano COS / Carlero D / Ortin J / Martin-Benito J | |||||||||
Funding support | Spain, 2 items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structural insights into influenza A virus ribonucleoproteins reveal a processive helical track as transcription mechanism. Authors: Rocío Coloma / Rocío Arranz / José M de la Rosa-Trevín / Carlos O S Sorzano / Sandie Munier / Diego Carlero / Nadia Naffakh / Juan Ortín / Jaime Martín-Benito / Abstract: The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein ...The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein arranged in a double helical conformation. vRNPs are macromolecular machines responsible for messenger RNA synthesis and genome replication, that is, the formation of progeny vRNPs. Here, we describe the structural basis of the transcription process. The mechanism, which we call the 'processive helical track', is based on the extreme flexibility of the helical part of the vRNP that permits a sliding movement between both antiparallel nucleoprotein-RNA strands, thereby allowing the polymerase to move over the genome while bound to both RNA ends. Accordingly, we demonstrate that blocking this movement leads to inhibition of vRNP transcriptional activity. This mechanism also reveals a critical role of the nucleoprotein in maintaining the double helical structure throughout the copying process to make the RNA template accessible to the polymerase. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4423.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-4423-v30.xml emd-4423.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_4423.png | 150.5 KB | ||
Others | emd_4423_additional.map.gz | 2.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4423 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4423 | HTTPS FTP |
-Related structure data
Related structure data | 6i7bMC 0175C 4412C 4426C 4430C 6h9gC 6i54C 6i7mC 6i85C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4423.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Inuenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation 3. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Local resolution map calculated using MonoRes software
File | emd_4423_additional.map | ||||||||||||
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Annotation | Local resolution map calculated using MonoRes software | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza A virus ribonucleoprotein
Entire | Name: Influenza A virus ribonucleoprotein |
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Components |
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-Supramolecule #1: Influenza A virus ribonucleoprotein
Supramolecule | Name: Influenza A virus ribonucleoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Influenza A virus (A/Wilson-Smith/1933(H1N1)) |
-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (A/Wilson-Smith/1933(H1N1)) |
Molecular weight | Theoretical: 53.114328 KDa |
Sequence | String: NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDPK KTGGPIYRRV DGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM DPRMCSLMQG STLPRRSGAA G AAVKGVGT ...String: NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDPK KTGGPIYRRV DGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM DPRMCSLMQG STLPRRSGAA G AAVKGVGT MVMELIRMIK RGINDRNFWR GENGRRTRIA YERMCNILKG KFQTAAQRTM VDQVRESRNP GNAEFEDLIF LA RSALILR GSVAHKSCLP ACVYGSAVAS GYDFEREGYS LVGIDPFRLL QNSQVYSLIR PNENPAHKSQ LVWMACHSAA FED LRVSSF IRGTKVVPRG KLSTRGVQIA SNENMETMES STLELRSRYW AIRTRSGGNT NQQRASSGQI SIQPTFSVQR NLPF DRPTI MAAFTGNTEG RTSDMRTEII RLMESARPED VSFQGRGVFE LSDEKATSPI VPSFDMSNEG SYFF |
-Macromolecule #2: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (A/Wilson-Smith/1933(H1N1)) |
Molecular weight | Theoretical: 2.107346 KDa |
Sequence | String: SSGQISIQPT FSVQRNLPF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 / Details: TN buffer (50 nM Tris-HCl, 150 mM KCl) |
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 3-68 / Number real images: 420 / Average electron dose: 2.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Segment selection | Number selected: 137461 / Software - Name: Xmipp / Details: Manual picking |
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CTF correction | Software - Name: CTFFIND |
Startup model | Type of model: OTHER Details: Initial model created using Iterative Helical Space Reconstruction protocols. |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 34.16 Å Applied symmetry - Helical parameters - Δ&Phi: -65.95 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 2.0) / Details: MonoRes software in Xmipp/Scipion / Number images used: 2867 |