+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16624 | |||||||||
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Title | HK97 Prohead II as part of a DNA packaging complex | |||||||||
Map data | HK97 bacteriophage prohead II i3 symmetry | |||||||||
Sample |
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Keywords | prohead / HK97 / bacteriophage / packaging / VIRAL PROTEIN | |||||||||
Function / homology | Phage capsid / Phage capsid family / Major capsid subunit Function and homology information | |||||||||
Biological species | Hendrixvirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Hawkins DEDP / Antson AA | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Insights into a viral motor: the structure of the HK97 packaging termination assembly. Authors: Dorothy E D P Hawkins / Oliver W Bayfield / Herman K H Fung / Daniel N Grba / Alexis Huet / James F Conway / Alfred A Antson / Abstract: Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each ...Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16624.map.gz | 386 MB | EMDB map data format | |
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Header (meta data) | emd-16624-v30.xml emd-16624.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16624_fsc.xml emd_16624_fsc_2.xml | 16.8 KB 21.7 KB | Display Display | FSC data file |
Images | emd_16624.png | 113.7 KB | ||
Masks | emd_16624_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-16624.cif.gz | 6.2 KB | ||
Others | emd_16624_half_map_1.map.gz emd_16624_half_map_2.map.gz | 335.5 MB 336.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16624 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16624 | HTTPS FTP |
-Validation report
Summary document | emd_16624_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16624_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16624_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | emd_16624_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16624 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16624 | HTTPS FTP |
-Related structure data
Related structure data | 8cfaMC 8cezC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16624.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | HK97 bacteriophage prohead II i3 symmetry | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4014 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16624_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: HK97 bacteriophage prohead II i3 symmetry
File | emd_16624_half_map_1.map | ||||||||||||
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Annotation | HK97 bacteriophage prohead II i3 symmetry | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HK97 bacteriophage prohead II i3 symmetry
File | emd_16624_half_map_2.map | ||||||||||||
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Annotation | HK97 bacteriophage prohead II i3 symmetry | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hendrixvirus
Entire | Name: Hendrixvirus |
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Components |
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-Supramolecule #1: Hendrixvirus
Supramolecule | Name: Hendrixvirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Proheads were produced by infection of E. coli 594 cells with HK97 amber mutant amC2, propagated using Escherichia LE392 cells. This map was derived from a prohead with portal and large terminase bound. NCBI-ID: 2169654 / Sci species name: Hendrixvirus / Sci species strain: HK97 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Escherichia phage EcSzw-2 (virus) |
Molecular weight | Theoretical: 560 KDa |
-Macromolecule #1: Major capsid subunit
Macromolecule | Name: Major capsid subunit / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Hendrixvirus |
Molecular weight | Theoretical: 42.286453 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: MSELALIQKA IEESQQKMTQ LFDAQKAEIE STGQVSKQLQ SDLMKVQEEL TKSGTRLFDL EQKLASGAEN PGEKKSFSER AAEELIKSW DGKQGTFGAK TFNKSLGSDA DSAGSLIQPM QIPGIIMPGL RRLTIRDLLA QGRTSSNALE YVREEVFTNN A DVVAEKAL ...String: MSELALIQKA IEESQQKMTQ LFDAQKAEIE STGQVSKQLQ SDLMKVQEEL TKSGTRLFDL EQKLASGAEN PGEKKSFSER AAEELIKSW DGKQGTFGAK TFNKSLGSDA DSAGSLIQPM QIPGIIMPGL RRLTIRDLLA QGRTSSNALE YVREEVFTNN A DVVAEKAL KPESDITFSK QTANVKTIAH WVQASRQVMD DAPMLQSYIN NRLMYGLALK EEGQLLNGDG TGDNLEGLNK VA TAYDTSL NATGDTRADI IAHAIYQVTE SEFSASGIVL NPRDWHNIAL LKDNEGRYIF GGPQAFTSNI MWGLPVVPTK AQA AGTFTV GGFDMASQVW DRMDATVEVS REDRDNFVKN MLTILCEERL ALAHYRPTAI IKGTFSSGS UniProtKB: Major capsid subunit |
-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: final buffer = 20 mM Tris pH 7.5, 10 mM MgCl2, 50 mM KGlu, 5 mM ATP-gamma-S |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV |
Details | Packaging reactions 30 nM hk97 proheads, 2.5 micromolar large terminase, 5 micromolar small terminase and 30 nM DNA, 75 micromolar ATP were incubated for 2 mins then 5 micromolar ATP-gamma-S was added. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |