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Yorodumi- EMDB-3403: Asymmetric cryo-EM reconstruction of phage MS2 reveals genome str... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3403 | |||||||||
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Title | Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ | |||||||||
Map data | Asymmetric reconstruction of MS2 virion | |||||||||
Sample |
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Keywords | MS2 / RNA genome / structure / cryo-EM | |||||||||
Biological species | Enterobacterio phage MS2 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 10.5 Å | |||||||||
Authors | Koning RI / Gomez-Blanco J / Akopjana I / Vargas J / Kazaks A / Tars K / Carazo JM / Koster AJ | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ. Authors: Roman I Koning / Josue Gomez-Blanco / Inara Akopjana / Javier Vargas / Andris Kazaks / Kaspars Tars / José María Carazo / Abraham J Koster / Abstract: In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes. Using cryo-electron microscopy and single particle analysis we determined the ...In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes. Using cryo-electron microscopy and single particle analysis we determined the asymmetric virion structure of bacteriophage MS2, which includes 178 copies of the coat protein, a single copy of the A-protein and the RNA genome. This reveals that in situ, the viral RNA genome can adopt a defined conformation. The RNA forms a branched network of stem-loops that almost all allocate near the capsid inner surface, while predominantly binding to coat protein dimers that are located in one-half of the capsid. This suggests that genomic RNA is highly involved in genome packaging and virion assembly. | |||||||||
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_3403.map.gz | 105.6 MB | EMDB map data format | |
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Header (meta data) | emd-3403-v30.xml emd-3403.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | EMD-3403.png | 198.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3403 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3403 | HTTPS FTP |
-Validation report
Summary document | emd_3403_validation.pdf.gz | 304.9 KB | Display | EMDB validaton report |
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Full document | emd_3403_full_validation.pdf.gz | 304 KB | Display | |
Data in XML | emd_3403_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3403 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3403 | HTTPS FTP |
-Related structure data
Related structure data | 3402C 3404C 3540C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10075 (Title: Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ Data size: 46.9 Data #1: Aligned 7-frame micrographs of bacteriophage MS2. [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3403.map.gz / Format: CCP4 / Size: 111 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Asymmetric reconstruction of MS2 virion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 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 : Bacteriophage MS2
Entire | Name: Bacteriophage MS2 (virus) |
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Components |
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-Supramolecule #1000: Bacteriophage MS2
Supramolecule | Name: Bacteriophage MS2 / type: sample / ID: 1000 / Details: Purified by gel filtration Oligomeric state: One copy of genomic RNA inside a shell of 178 capsid proteins and one A-protein Number unique components: 1 |
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Molecular weight | Theoretical: 3.6 MDa |
-Supramolecule #1: Enterobacterio phage MS2
Supramolecule | Name: Enterobacterio phage MS2 / type: virus / ID: 1 / Name.synonym: bacteriophage MS2 / NCBI-ID: 12022 / Sci species name: Enterobacterio phage MS2 / Virus type: VIRION / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage MS2 / Sci species subspecies: Enterobacterio phage MS2 |
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Host (natural) | Organism: Escherichia coli (E. coli) / Strain: XL-1 blue / synonym: BACTERIA(EUBACTERIA) |
Molecular weight | Theoretical: 3.6 MDa |
Virus shell | Shell ID: 1 / Name: MS2 / Diameter: 275 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Staining | Type: NEGATIVE / Details: Vitrification |
Grid | Details: Cu 300 Mesh with quantifoil R2/2 support film, glow discharged in air at 0.2 mbar for 1 minute at 30 mA. |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 70 % / Chamber temperature: 100 K / Instrument: LEICA EM GP Method: Blotted using filter paper for 1 to 2 seconds before blotting |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77 K / Max: 97 K / Average: 87 K |
Alignment procedure | Legacy - Astigmatism: Cs corrector / Legacy - Electron beam tilt params: 15 |
Date | May 19, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 751 / Average electron dose: 35 e/Å2 Details: Images are average of 7 frames recorded in movie mode on direct electron detector Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 61403 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.02 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Movies were aligned using Optical Flow, CTFs were estimated using CTFFIND3, and were used to select the best quality micrographs. A total of 22,441 particles were picked automatically using Xmipp. Particles were classified using 2D reference-free Relion approach. Relion was used for 3D refinement using icosahedral symmetry and gold-standard approach. |
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CTF correction | Details: Per image |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: OTHER / Software - Name: Scipion, Xmipp, CTFFIND3, Relion / Number images used: 18977 |
Final two d classification | Number classes: 5201 |