+Open data
-Basic information
Entry | Database: PDB / ID: 8pop | ||||||
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Title | HK97 small terminase in complex with DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / small terminase / HK97 / bacteriophage / complex with DNA | ||||||
Function / homology | DNA / DNA (> 10) / Terminase small subunit Function and homology information | ||||||
Biological species | Escherichia phage HK97 (virus) Byrnievirus HK97 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Chechik, M. / Greive, S.J. / Antson, A.A. / Jenkins, H.T. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structural basis for DNA recognition by a viral genome-packaging machine. Authors: Maria Chechik / Sandra J Greive / Alfred A Antson / Huw T Jenkins / Abstract: DNA recognition is critical for assembly of double-stranded DNA viruses, particularly for the initiation of packaging the viral genome into the capsid. The key component that recognizes viral DNA is ...DNA recognition is critical for assembly of double-stranded DNA viruses, particularly for the initiation of packaging the viral genome into the capsid. The key component that recognizes viral DNA is the small terminase protein. Despite prior studies, the molecular mechanism for DNA recognition remained elusive. Here, we address this question by identifying the minimal site in the bacteriophage HK97 genome specifically recognized by the small terminase and determining the structure of this complex by cryoEM. The circular small terminase employs an entirely unexpected mechanism in which DNA transits through the central tunnel, and sequence-specific recognition takes place as it emerges. This recognition stems from a substructure formed by the N- and C-terminal segments of two adjacent protomers which are unstructured when DNA is absent. Such interaction ensures continuous engagement of the small terminase with DNA, enabling it to slide along the DNA while simultaneously monitoring its sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the specific sequence. #1: 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pop.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pop.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pop_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8pop_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8pop_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 8pop_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/8pop ftp://data.pdbj.org/pub/pdb/validation_reports/po/8pop | HTTPS FTP |
-Related structure data
Related structure data | 17794MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
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