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Yorodumi- EMDB-2207: Negative stained electron microscopy reconstruction of the viral ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2207 | |||||||||
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Title | Negative stained electron microscopy reconstruction of the viral polymerase of influenza A virus ribonucleoprotein isolated from virions. Conformation 1. | |||||||||
Map data | Influenza virus polymerase. Conformation 1. | |||||||||
Sample |
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Keywords | Influenza / ribonucleoprotein / polymerase / RNA polymerase / nucleoprotein / negative stained electron microscopy / RNA. | |||||||||
Biological species | Influenza A virus | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Arranz R / Coloma R / Chichon FJ / Conesa JJ / Carrascosa JL / Valpuesta JM / Ortin J / Martin-Benito J | |||||||||
Citation | Journal: Science / Year: 2012 Title: The structure of native influenza virion ribonucleoproteins. Authors: Rocío Arranz / Rocío Coloma / Francisco Javier Chichón / José Javier Conesa / José L Carrascosa / José M Valpuesta / Juan Ortín / Jaime Martín-Benito / Abstract: The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with ...The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with the polymerase complex and nucleoprotein (NP), forming ribonucleoproteins (RNPs), which are responsible for virus transcription and replication. We describe the structure of native RNPs derived from virions. They show a double-helical conformation in which two NP strands of opposite polarity are associated with each other along the helix. Both strands are connected by a short loop at one end of the particle and interact with the polymerase complex at the other end. This structure will be relevant for unraveling the mechanisms of nuclear import of parental virus RNPs, their transcription and replication, and the encapsidation of progeny RNPs into virions. | |||||||||
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_2207.map.gz | 951.4 KB | EMDB map data format | |
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Header (meta data) | emd-2207-v30.xml emd-2207.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | 2207_image_EM2207.tif | 198.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2207 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2207 | HTTPS FTP |
-Validation report
Summary document | emd_2207_validation.pdf.gz | 229.7 KB | Display | EMDB validaton report |
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Full document | emd_2207_full_validation.pdf.gz | 228.9 KB | Display | |
Data in XML | emd_2207_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2207 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2207 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2207.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Influenza virus polymerase. Conformation 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1...
Entire | Name: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1). Polymerase end. Conformation 1. |
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Components |
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-Supramolecule #1000: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1...
Supramolecule | Name: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1). Polymerase end. Conformation 1. type: sample / ID: 1000 / Number unique components: 5 |
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-Macromolecule #1: PB1
Macromolecule | Name: PB1 / type: protein_or_peptide / ID: 1 / Name.synonym: PB1 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Influenza A virus / Strain: A/WSN/33 (H1N1) |
Molecular weight | Experimental: 86 KDa / Theoretical: 86 KDa |
-Macromolecule #2: PA
Macromolecule | Name: PA / type: protein_or_peptide / ID: 2 / Name.synonym: PA / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Influenza A virus / Strain: A/WSN/33 (H1N1) |
Molecular weight | Experimental: 83 KDa / Theoretical: 83 KDa |
-Macromolecule #3: PB2
Macromolecule | Name: PB2 / type: protein_or_peptide / ID: 3 / Name.synonym: PB2 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Influenza A virus / Strain: A/WSN/33 (H1N1) |
Molecular weight | Experimental: 86 KDa / Theoretical: 86 KDa |
-Macromolecule #4: nucleoprotein
Macromolecule | Name: nucleoprotein / type: protein_or_peptide / ID: 4 / Name.synonym: nucleoprotein / Recombinant expression: No |
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Source (natural) | Organism: Influenza A virus / Strain: A/WSN/33 (H1N1) |
Molecular weight | Theoretical: 56 KDa |
-Macromolecule #5: RNA
Macromolecule | Name: RNA / type: rna / ID: 5 / Name.synonym: RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Influenza A virus |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: 50mM Tris-HCl, 100mM KCl, 5mM MgCl2, 0.5% Igepal, 150mM imidazole |
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Staining | Type: NEGATIVE Details: Samples were applied to one side of a carbon coated Cu/Rh grid and stained on 2% w/v uranyl acetate for 90 seconds. |
Grid | Details: Freshly carbon coated, glow discharged for 15 seconds. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | May 1, 2011 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1024 / Details: downsampling factor 2. / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 65000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each plate |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: XMIPP / Number images used: 7074 |