+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29392 | |||||||||
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Title | portal vertex of HK97 phage | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Prohead I / icosahedral symmetry / HK97 / phage / capsid / VIRUS | |||||||||
Function / homology | Phage portal protein, HK97 / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral capsid / Portal protein Function and homology information | |||||||||
Biological species | Escherichia phage HK97 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Huet A / Oh B / Maurer J / Duda RL / Conway JF | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2023 Title: A symmetry mismatch unraveled: How phage HK97 scaffold flexibly accommodates a 12-fold pore at a 5-fold viral capsid vertex. Authors: Alexis Huet / Bonnie Oh / Josh Maurer / Robert L Duda / James F Conway / Abstract: Tailed bacteriophages and herpesviruses use a transient scaffold to assemble icosahedral capsids with hexameric capsomers on the faces and pentameric capsomers at all but one vertex where a 12-fold ...Tailed bacteriophages and herpesviruses use a transient scaffold to assemble icosahedral capsids with hexameric capsomers on the faces and pentameric capsomers at all but one vertex where a 12-fold portal is thought to nucleate the assembly. How does the scaffold orchestrate this step? We have determined the portal vertex structure of the bacteriophage HK97 procapsid, where the scaffold is a domain of the major capsid protein. The scaffold forms rigid helix-turn-strand structures on the interior surfaces of all capsomers and is further stabilized around the portal, forming trimeric coiled-coil towers, two per surrounding capsomer. These 10 towers bind identically to 10 of 12 portal subunits, adopting a pseudo-12-fold organization that explains how the symmetry mismatch is managed at this early step. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29392.map.gz | 228.3 MB | EMDB map data format | |
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Header (meta data) | emd-29392-v30.xml emd-29392.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29392_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_29392.png | 187.6 KB | ||
Filedesc metadata | emd-29392.cif.gz | 5.8 KB | ||
Others | emd_29392_half_map_1.map.gz emd_29392_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29392 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29392 | HTTPS FTP |
-Validation report
Summary document | emd_29392_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_29392_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_29392_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_29392_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29392 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29392 | HTTPS FTP |
-Related structure data
Related structure data | 8fqlMC 8fqkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29392.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29392_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29392_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Escherichia phage HK97
Entire | Name: Escherichia phage HK97 (virus) |
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Components |
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-Supramolecule #1: Escherichia phage HK97
Supramolecule | Name: Escherichia phage HK97 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Prohead I expressed from plasmid in E.Coli / NCBI-ID: 2681617 / Sci species name: Escherichia phage HK97 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 17.7 MDa |
Virus shell | Shell ID: 1 / Name: Prohead I / Diameter: 500.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage HK97 (virus) |
Molecular weight | Theoretical: 47.318488 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEEPKYTIDL RTNNGWWARL KSWFVGGRLV TPNQGSQTGP VSAHGYLGDS SINDERILQI STVWRCVSLI STLTACLPLD VFETDQNDN RKKVDLSNPL ARLLRYSPNQ YMTAQEFREA MTMQLCFYGN AYALVDRNSA GDVISLLPLQ SANMDVKLVG K KVVYRYQR ...String: MEEPKYTIDL RTNNGWWARL KSWFVGGRLV TPNQGSQTGP VSAHGYLGDS SINDERILQI STVWRCVSLI STLTACLPLD VFETDQNDN RKKVDLSNPL ARLLRYSPNQ YMTAQEFREA MTMQLCFYGN AYALVDRNSA GDVISLLPLQ SANMDVKLVG K KVVYRYQR DSEYADFSQK EIFHLKGFGF TGLVGLSPIA FACKSAGVAV AMEDQQRDFF ANGAKSPQIL STGEKVLTEQ QR SQVEENF KEIAGGPVKK RLWILEAGFS TSAIGVTPQD AEMMASRKFQ VSELARFFGV PPHLVGDVEK STSWGSGIEQ QNL GFLQYT LQPYISRWEN SIQRWLIPSK DVGRLHAEHN LDGLLRGDSA SRAAFMKAMG ESGLRTINEM RRTDNMPPLP GGDV AMRQA QYVPITDLGT NKEPRNNGA UniProtKB: Portal protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2909 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8fql: |