8POP image
Deposition Date 2023-07-05
Release Date 2023-08-09
Last Version Date 2024-08-21
Entry Detail
PDB ID:
8POP
Title:
HK97 small terminase in complex with DNA
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Terminase small subunit
Gene (Uniprot):1
Chain IDs:A, B, C, D, E, F, G, H, I
Chain Length:161
Number of Molecules:9
Biological Source:Escherichia phage HK97
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (31-MER)
Chain IDs:J
Chain Length:31
Number of Molecules:1
Biological Source:Byrnievirus HK97
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (31-MER)
Chain IDs:K
Chain Length:31
Number of Molecules:1
Biological Source:Byrnievirus HK97
Ligand Molecules
Primary Citation
Structural basis for DNA recognition by a viral genome-packaging machine.
Proc.Natl.Acad.Sci.USA 121 e2406138121 e2406138121 (2024)
PMID: 39116131 DOI: 10.1073/pnas.2406138121

Abstact

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 cos sequence.

Legend

Protein

Chemical

Disease

Primary Citation of related structures