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Yorodumi- EMDB-4430: Helical part of the influenza A virus ribonucleoprotein. Conforma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4430 | |||||||||
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Title | Helical part of the influenza A virus ribonucleoprotein. Conformation 5. | |||||||||
Map data | Helical part of influenza A ribonucleoprotein. Conformation 5. | |||||||||
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)) / Influenza A virus (strain A/Wilson-Smith/1933 H1N1) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 24.0 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_4430.map.gz | 6.1 MB | EMDB map data format | |
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Header (meta data) | emd-4430-v30.xml emd-4430.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_4430.png | 127.6 KB | ||
Filedesc metadata | emd-4430.cif.gz | 6.2 KB | ||
Others | emd_4430_additional.map.gz | 2.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4430 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4430 | HTTPS FTP |
-Validation report
Summary document | emd_4430_validation.pdf.gz | 231.3 KB | Display | EMDB validaton report |
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Full document | emd_4430_full_validation.pdf.gz | 230.4 KB | Display | |
Data in XML | emd_4430_validation.xml.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4430 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4430 | HTTPS FTP |
-Related structure data
Related structure data | 6i85MC 0175C 4412C 4423C 4426C 6h9gC 6i54C 6i7bC 6i7mC 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_4430.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Helical part of influenza A ribonucleoprotein. Conformation 5. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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. Vilas...
File | emd_4430_additional.map | ||||||||||||
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Annotation | Local resolution map calculated using MonoRes software. Vilas et al. Structure. 2018 Feb 6;26(2):337-344. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helical part of Influenza A virus ribonucleoprotein.
Entire | Name: Helical part of Influenza A virus ribonucleoprotein. |
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Components |
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-Supramolecule #1: Helical part of Influenza A virus ribonucleoprotein.
Supramolecule | Name: Helical part of 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: Influenza A nucleoprotein
Macromolecule | Name: Influenza A nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (strain A/Wilson-Smith/1933 H1N1) |
Molecular weight | Theoretical: 45.098555 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 TSDMRTEIIR LMESARPEDV SFQGRGVFEL SDEKATSPIV PSFDMSNEGS YFF UniProtKB: Nucleoprotein |
-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 (strain A/Wilson-Smith/1933 H1N1) |
Molecular weight | Theoretical: 2.964355 KDa |
Sequence | String: SSGQISIQPT FSVQRNLPFD RPTIMAA UniProtKB: Nucleoprotein |
-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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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 | Applied symmetry - Helical parameters - Δz: 25.18 Å Applied symmetry - Helical parameters - Δ&Phi: -65.15 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 2.0) / Number images used: 408 |
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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-6i85: |