8APL
Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C6
Summary for 8APL
| Entry DOI | 10.2210/pdb8apl/pdb |
| EMDB information | 15574 |
| Descriptor | Primase D5 (1 entity in total) |
| Functional Keywords | dna helicase, d5_n domain, duf5906 domain, pox_d5 domain, sf3 helicase, viral protein |
| Biological source | Vaccinia virus Copenhagen |
| Total number of polymer chains | 6 |
| Total formula weight | 320971.71 |
| 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: 2024-07-24) |
| 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 Cited by 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: 36298761DOI: 10.3390/v14102206 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (4.1 Å) |
Structure validation
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