8APM image
Entry Detail
PDB ID:
8APM
EMDB ID:
Keywords:
Title:
Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C1
Biological Source:
PDB Version:
Deposition Date:
2022-08-10
Release Date:
2022-11-09
Method Details:
Experimental Method:
Resolution:
6.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Primase D5
Mutations:L221A, D222M
Chain IDs:A, B (auth: E), C (auth: D), D (auth: B), E (auth: C), F
Chain Length:465
Number of Molecules:6
Biological Source:Vaccinia virus Copenhagen
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*CP*CP*GP*AP*AP*TP*CP*A)-3')
Chain IDs:G (auth: X)
Chain Length:30
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*TP*GP*AP*TP*TP*CP*GP*G)-3')
Mutations:G2A
Chain IDs:H (auth: Y)
Chain Length:30
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.
Viruses 14 ? ? (2022)
PMID: 36298761 DOI: 10.3390/v14102206

Abstact

Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.

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Primary Citation of related structures