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Yorodumi- EMDB-2112: Maturation in action: CryoEM study of a viral capsid caught durin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2112 | |||||||||
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Title | Maturation in action: CryoEM study of a viral capsid caught during expansion. (The HK97 first expansion intermediate). | |||||||||
Map data | Reconstruction of the phage HK97 first expansion intermediate harboring E-loop truncated coat subunits. | |||||||||
Sample |
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Keywords | virus maturation / capsid / bacteriophage HK97 / quasi-equivalence / electron cryomicroscopy | |||||||||
Biological species | Enterobacteria phage HK97 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.3 Å | |||||||||
Authors | Veesler D / Quispe J / Grigorieff N / Potter CS / Carragher B / Johnson JE | |||||||||
Citation | Journal: Structure / Year: 2012 Title: Maturation in action: CryoEM study of a viral capsid caught during expansion. Authors: David Veesler / Joel Quispe / Nikolaus Grigorieff / Clinton S Potter / Bridget Carragher / John E Johnson / Abstract: Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of ...Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of a metastable prohead, poised for exothermic expansion triggered by DNA packaging. During maturation, the capsid subunit transitions from a strained to a canonical tertiary conformation and this has been postulated to be the driving mechanism for initiating expansion via switching hexameric capsomer architecture from skewed to 6-fold symmetric. We report the subnanometer electron-cryomicroscopy reconstruction of the HK97 first expansion intermediate before any crosslink formation. This form displays 6-fold symmetric hexamers, but capsid subunit tertiary structures exhibit distortions comparable to the prohead forms. We propose that coat subunit strain release acts in synergy with the first crosslinks to drive forward maturation. Finally, we speculate that the energetic features of this transition may result from increased stability of intermediates during maturation via enhanced inter-subunit interactions. | |||||||||
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_2112.map.gz | 150.9 MB | EMDB map data format | |
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Header (meta data) | emd-2112-v30.xml emd-2112.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | 2112.png | 178.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2112 | HTTPS FTP |
-Validation report
Summary document | emd_2112_validation.pdf.gz | 252.6 KB | Display | EMDB validaton report |
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Full document | emd_2112_full_validation.pdf.gz | 251.7 KB | Display | |
Data in XML | emd_2112_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2112 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2112 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2112.map.gz / Format: CCP4 / Size: 162.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the phage HK97 first expansion intermediate harboring E-loop truncated coat subunits. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : HK97 Expansion intermediate 1 (E-loop truncated mutant)
Entire | Name: HK97 Expansion intermediate 1 (E-loop truncated mutant) |
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Components |
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-Supramolecule #1000: HK97 Expansion intermediate 1 (E-loop truncated mutant)
Supramolecule | Name: HK97 Expansion intermediate 1 (E-loop truncated mutant) type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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Molecular weight | Theoretical: 12.5 MDa |
-Macromolecule #1: HK97 gp5
Macromolecule | Name: HK97 gp5 / type: protein_or_peptide / ID: 1 / Details: The capsid harbor E-loop truncated coat subunits / Oligomeric state: icosahedral / Recombinant expression: Yes |
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Source (natural) | Organism: Enterobacteria phage HK97 (virus) |
Molecular weight | Theoretical: 12.5 MDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pT7-5Hd2.9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 11 mg/mL |
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Buffer | pH: 7.5 / Details: 10mM Tris, 40mM NaCl |
Grid | Details: C-flat |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 94 K / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 50000 times magnification |
Date | Oct 28, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 1714 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 62900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.6 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder: Liquid Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: whole micrograph |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign / Details: The final map was calculated from a single dataset / Number images used: 17116 |