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Yorodumi- EMDB-5765: A new topology of the HK97-like fold revealed in Bordetella bacte... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5765 | |||||||||
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Title | A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5A resolution | |||||||||
Map data | Averaged MCP density of Bordetella bacteriophage (EMD-5764) | |||||||||
Sample |
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Keywords | Protein topology / HK97 like / cryoEM / bacteriophage | |||||||||
Biological species | Bordetella phage BPP-1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhang X / Guo H / Jin L / Czornyj E / Hodes A / Hui WH / Nieh AW / Miller JF / Zhou ZH | |||||||||
Citation | Journal: Elife / Year: 2013 Title: A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution. Authors: Xing Zhang / Huatao Guo / Lei Jin / Elizabeth Czornyj / Asher Hodes / Wong H Hui / Angela W Nieh / Jeff F Miller / Z Hong Zhou / Abstract: Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering ...Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like ('Johnson') for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001. | |||||||||
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_5765.map.gz | 218.5 KB | EMDB map data format | |
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Header (meta data) | emd-5765-v30.xml emd-5765.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_5765.jpg | 145 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5765 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5765 | HTTPS FTP |
-Validation report
Summary document | emd_5765_validation.pdf.gz | 79.2 KB | Display | EMDB validaton report |
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Full document | emd_5765_full_validation.pdf.gz | 78.3 KB | Display | |
Data in XML | emd_5765_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5765 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5765 | HTTPS FTP |
-Related structure data
Related structure data | 5764C 5766C 3j4uFC F: fitted*YM C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5765.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Averaged MCP density of Bordetella bacteriophage (EMD-5764) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 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 : Bordetella bacteriophage major capsid protein (MCP)
Entire | Name: Bordetella bacteriophage major capsid protein (MCP) |
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Components |
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-Supramolecule #1000: Bordetella bacteriophage major capsid protein (MCP)
Supramolecule | Name: Bordetella bacteriophage major capsid protein (MCP) / type: sample / ID: 1000 / Details: This is the averaged MCP density of EMD-5764. / Number unique components: 1 |
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-Macromolecule #1: major capsid protein
Macromolecule | Name: major capsid protein / type: protein_or_peptide / ID: 1 / Name.synonym: MCP / Details: This is the averaged MCP density of EMD-5764. / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bordetella phage BPP-1 (virus) / synonym: Bordetella bacteriophage |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 50 mM Tris-HCl, 250 mM NaCl |
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Grid | Details: 400 mesh holey carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 80 K |
Alignment procedure | Legacy - Astigmatism: manual correction / Legacy - Electron beam tilt params: 0 |
Date | Jul 12, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 895 / Average electron dose: 25 e/Å2 / Bits/pixel: 2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 57660 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: eLite3D, Frealign / Details: This is the averaged MCP density of EMD-5764. / Number images used: 39549 |
Final two d classification | Number classes: 1 |