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Yorodumi- EMDB-4412: Helical part of the influenza A virus ribonucleoprotein. Conforma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4412 | |||||||||
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Title | Helical part of the influenza A virus ribonucleoprotein. Conformation 2. | |||||||||
Map data | Influenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation s. | |||||||||
Sample |
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Keywords | Influenza A virus Ribonucleoprotein RNA binding protein / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / host cell / 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 | |||||||||
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_4412.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-4412-v30.xml emd-4412.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_4412.png | 158.1 KB | ||
Filedesc metadata | emd-4412.cif.gz | 6.3 KB | ||
Others | emd_4412_additional.map.gz | 2.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4412 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4412 | HTTPS FTP |
-Validation report
Summary document | emd_4412_validation.pdf.gz | 235.6 KB | Display | EMDB validaton report |
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Full document | emd_4412_full_validation.pdf.gz | 234.8 KB | Display | |
Data in XML | emd_4412_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4412 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4412 | HTTPS FTP |
-Related structure data
Related structure data | 6i54MC 0175C 4423C 4426C 4430C 6h9gC 6i7bC 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_4412.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Influenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation s. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Resolution map.
File | emd_4412_additional.map | ||||||||||||
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Annotation | Resolution map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza A virus
Entire | Name: Influenza A virus |
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Components |
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-Supramolecule #1: Influenza A virus
Supramolecule | Name: Influenza A virus / 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: 43.079227 KDa |
Sequence | String: NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDD ATAGLTHMMI WHSNLNDATY QRTRALVRTG MDPRMCSLMQ GSTLPRRSGA AGAAVKGVGT MVMELIRMIK R GINRRTRI ...String: NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDD ATAGLTHMMI WHSNLNDATY QRTRALVRTG MDPRMCSLMQ GSTLPRRSGA AGAAVKGVGT MVMELIRMIK R GINRRTRI AYERMCNILK GKFQTAAQRT MVDQVRESRN PGNAEFEDLI FLARSALILR GSVAHKSCLP ACVYGSAVAS GY DFEREGY SLVGIDPFRL LQNSQVYSLI RPNENPAHKS QLVWMACHSA AFEDLRVSSF IRGTKVVPRG KLSTRGVQIA SNE NMETME SSTLELRSRY WAIRTRSGGN TDVSFQGRGV FELSDEKATS PIVPSFDMSN EGSYFF UniProtKB: Nucleoprotein |
-Macromolecule #2: Influenza virus nucleoprotein
Macromolecule | Name: Influenza virus 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 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl / Component - Name: TN buffer / Details: TN buffer (50 mM Tris-HCl, 150 mM KCl) |
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 3-68 / Number grids imaged: 1 / Number real images: 420 / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number classes used: 1 Applied symmetry - Helical parameters - Δz: 34.47 Å Applied symmetry - Helical parameters - Δ&Phi: -68.33 ° 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: Local resolution calculated using MonoRes software. Vilas et al. Structure. 2018 Feb 6;26(2):337-344.e4. doi: 10.1016/j.str Number images used: 4806 |
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Segment selection | Number selected: 137461 / Software - Name: Xmipp (ver. 3.0) / Details: Manual picking |
Startup model | Type of model: OTHER Details: Initial model created using Iterative Helical Real Space Reconstruction |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0) |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-6i54: |