{"entity": "researcher", "timestamp": "2026-07-12T18:07:49.202Z", "family": "Raia", "given": "Pierre", "initials": "P", "orcid": "0000-0003-3469-1922", "affiliations": ["Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.", "Sorbonne Universit\u00e9, \u00c9cole Doctorale Complexit\u00e9 du Vivant (ED515), Paris, France."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/bdf3d3b11b384d52ba1bc00e7173b44b.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/bdf3d3b11b384d52ba1bc00e7173b44b"}}, "publications": [{"entity": "publication", "iuid": "f4b79cf485ae4ae2b999a8ce542884b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4b79cf485ae4ae2b999a8ce542884b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4b79cf485ae4ae2b999a8ce542884b9"}}, "title": "Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.", "authors": [{"family": "Madru", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Henneke", "given": "Ghislaine", "initials": "G"}, {"family": "Raia", "given": "Pierre", "initials": "P", "orcid": "0000-0003-3469-1922", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdf3d3b11b384d52ba1bc00e7173b44b.json"}}, {"family": "Hugonneau-Beaufet", "given": "In\u00e8s", "initials": "I"}, {"family": "Pehau-Arnaudet", "given": "G\u00e9rard", "initials": "G"}, {"family": "England", "given": "Patrick", "initials": "P"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Delarue", "given": "Marc", "initials": "M"}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Sauguet", "given": "Ludovic", "initials": "L"}], "type": "journal article", "published": "2020-03-27", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "1591", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD-PCNA complex from Pyrococcus abyssi at 3.77 \u00c5. Using an integrative structural biology approach - combining cryo-EM, X-ray crystallography, protein-protein interaction measurements, and activity assays - we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Pol\u03b1 replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication.", "doi": "10.1038/s41467-020-15392-9", "pmid": "32221299", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15392-9"}, {"db": "pmc", "key": "PMC7101311"}], "notes": [], "created": "2020-04-16T10:31:32.697Z", "modified": "2021-11-10T12:52:47.618Z"}, {"entity": "publication", "iuid": "cd2c79c36dce474887bcfa22c3b80b5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd2c79c36dce474887bcfa22c3b80b5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd2c79c36dce474887bcfa22c3b80b5d"}}, "title": "Structure of the DP1\u2013DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases", "authors": [{"family": "Raia", "given": "Pierre", "initials": "P", "orcid": "0000-0003-3469-1922", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdf3d3b11b384d52ba1bc00e7173b44b.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Henry", "given": "Etienne", "initials": "E"}, {"family": "Pehau-Arnaudet", "given": "G\u00e9rard", "initials": "G"}, {"family": "Br\u00fbl\u00e9", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0002-8797-6748", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4434962f7e74f27912471002ac84cf4.json"}}, {"family": "B\u00e9guin", "given": "Pierre", "initials": "P"}, {"family": "Henneke", "given": "Ghislaine", "initials": "G"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Delarue", "given": "Marc", "initials": "M"}, {"family": "Sauguet", "given": "Ludovic", "initials": "L", "orcid": "0000-0002-1259-6601", "researcher": {"href": "https://publications.scilifelab.se/researcher/157797855bd0495db5f788432d1e330f.json"}}], "type": "journal-article", "published": "2019-01-18", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "17", "issue": "1", "pages": "e3000122", "issn-l": "1544-9173"}, "abstract": "PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.", "doi": "10.1371/journal.pbio.3000122", "pmid": "30657780", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PBIOLOGY-D-18-00775"}, {"db": "pmc", "key": "PMC6355029"}], "notes": [], "created": "2019-02-12T09:40:03.456Z", "modified": "2021-06-21T13:42:01.143Z"}]}