+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17818 | |||||||||
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Title | Complex of HK97 small terminase with DNA | |||||||||
Map data | HK97 small terminase in complex with DNA | |||||||||
Sample |
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Keywords | HK97 small terminase / bacteriophage / protein:DNA complex / cryoEM structure / DNA BINDING PROTEIN | |||||||||
Function / homology | Terminase small subunit Function and homology information | |||||||||
Biological species | Byrnievirus HK97 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
Authors | Chechik M / Greive SJ / Antson AA / Jenkins HT | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structure of HK97 small terminase:DNA complex unveils a novel DNA binding mechanism by a circular protein. Authors: Maria Chechik / Sandra J Greive / Alfred A Antson / Huw T Jenkins / Abstract: DNA recognition is critical for assembly of double-stranded DNA viruses, in particular for the initiation of packaging the viral genome into the capsid. DNA packaging has been extensively studied for ...DNA recognition is critical for assembly of double-stranded DNA viruses, in particular for the initiation of packaging the viral genome into the capsid. DNA packaging has been extensively studied for three archetypal bacteriophage systems: , and phi29. We identified the minimal site within the region of bacteriophage HK97 specifically recognised by the small terminase and determined a cryoEM structure for the small terminase:DNA complex. This nonameric circular protein utilizes a previously unknown mechanism of DNA binding. While DNA threads through the central tunnel, unexpectedly, DNA-recognition is generated at its exit by a substructure formed by the N- and C-terminal segments of two adjacent protomers of the terminase which are unstructured in the absence of DNA. Such interaction ensures continuous engagement of the small terminase with DNA, allowing sliding along DNA while simultaneously checking the DNA sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the site. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17818.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-17818-v30.xml emd-17818.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17818_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_17818.png | 54.2 KB | ||
Masks | emd_17818_msk_1.map | 8 MB | Mask map | |
Others | emd_17818_half_map_1.map.gz emd_17818_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17818 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17818 | HTTPS FTP |
-Related structure data
Related structure data | 8popC 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_17818.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | HK97 small terminase in complex with DNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.18889 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17818_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: HK97 small terminase in complex with DNA
File | emd_17818_half_map_1.map | ||||||||||||
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Annotation | HK97 small terminase in complex with DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HK97 small terminase in complex with DNA
File | emd_17818_half_map_2.map | ||||||||||||
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Annotation | HK97 small terminase in complex with DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : complex of HK97 with DNA
Entire | Name: complex of HK97 with DNA |
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Components |
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-Supramolecule #1: complex of HK97 with DNA
Supramolecule | Name: complex of HK97 with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Byrnievirus HK97 |
Molecular weight | Theoretical: 185 KDa |
-Macromolecule #1: small terminase
Macromolecule | Name: small terminase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Byrnievirus HK97 |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MADKRIRSDS SAAAVQAMKN AAVDTIDPPS HAGLEKKAEP FWHDNIRSKA LDSWTPADLL AAVELANNQ LYITVLRKDL RKEERIRGEE RDEGLIKDLR KQIVELQRTI LAQRRDLQIH S HATNGESR DQKKRNQNDR DARNTKNEHQ DQDDNLIAFP KHG UniProtKB: Terminase small subunit |
-Macromolecule #2: DNA (31-mer)
Macromolecule | Name: DNA (31-mer) / type: dna / ID: 2 / Classification: DNA |
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Source (natural) | Organism: Byrnievirus HK97 |
Sequence | String: TAAAACTAAA AAAATCGGGT TAGCGTTAAA T |
-Macromolecule #3: DNA (31-mer)
Macromolecule | Name: DNA (31-mer) / type: dna / ID: 3 / Classification: DNA |
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Source (natural) | Organism: Byrnievirus HK97 |
Sequence | String: ATTTAACGCT AACCCGATTT TTTTAGTTTT A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | complex was purified on S200 10/300 column |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2767 / Average exposure time: 8.0 sec. / Average electron dose: 53.6 e/Å2 Details: Two datasets were collected: 1st dataset: 682 images 2nd dataset: 2085 images |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |