8APM

Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C1

Summary for 8APM

• Entry DOI: 10.2210/pdb8apm/pdb
• EMDB information: 15575
• Descriptor: Primase D5, DNA (5'-D(P*CP*CP*GP*AP*AP*TP*CP*A)-3'), DNA (5'-D(P*TP*GP*AP*TP*TP*CP*GP*G)-3') (3 entities in total)
• Functional Keywords: dna helicase, d5_n domain, duf5906 domain, pox_d5 domain, sf3 helicase, viral protein
• Biological source: Vaccinia virus Copenhagen; More
• Total number of polymer chains: 8
• Total formula weight: 339449.61

Authors

Burmeister, W.P.,Hutin, S.,Ling, W.L.,Grimm, C.,Schoehn, G. (deposition date: 2022-08-10, release date: 2022-11-09, Last modification date: 2023-08-16)

Primary citation

Hutin, S.,Ling, W.L.,Tarbouriech, N.,Schoehn, G.,Grimm, C.,Fischer, U.,Burmeister, W.P.
The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.
Viruses, 14:-, 2022

PubMed Abstract: 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.

PubMed: 36298761
DOI: 10.3390/v14102206

Experimental method

ELECTRON MICROSCOPY (6.6 Å)