{"doi":"10.1016/j.jmb.2008.10.012","title":"Visualization of Bacteriophage T3 Capsids with DNA Incompletely Packaged In Vivo","abstract":null,"journal":"Journal of Molecular Biology","year":2008,"id":618638,"datarank":0.519860385419959,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.0,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1146477,"name":"Elena T. Wright","orcid":null,"position":1,"is_corresponding":false},{"id":123432,"name":"Susan T. Weintraub","orcid":null,"position":2,"is_corresponding":false},{"id":1596043,"name":"Kevin Hakala","orcid":null,"position":3,"is_corresponding":false},{"id":1358334,"name":"Weimin Wu","orcid":"0000-0003-1565-0471","position":4,"is_corresponding":false},{"id":1146151,"name":"Philip Serwer","orcid":"0000-0002-8990-3251","position":5,"is_corresponding":false},{"id":342604,"name":"Wen Jiang","orcid":"0000-0002-1292-2411","position":6,"is_corresponding":false},{"id":1596042,"name":"Ping-An Fang","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Visualization of Bacteriophage T3 Capsids with DNA Incompletely Packaged In Vivo","abstract":"The tightly packaged double-stranded DNA (dsDNA) genome in the mature particles of many tailed bacteriophages has been shown to form multiple concentric rings when reconstructed from cryo-electron micrographs. However, recent single-particle DNA packaging force measurements have suggested that incompletely packaged DNA (ipDNA) is less ordered when it is shorter than approximately 25% of the full genome length. The study presented here initially achieves both the isolation and the ipDNA length-based fractionation of ipDNA-containing T3 phage capsids (ipDNA-capsids) produced by DNA packaging in vivo; some ipDNA has quantized lengths, as judged by high-resolution gel electrophoresis of expelled DNA. This is the first isolation of such particles among the tailed dsDNA bacteriophages. The ipDNA-capsids are a minor component (containing approximately 10(-4) of packaged DNA in all particles) and are initially detected by nondenaturing gel electrophoresis after partial purification by buoyant density centrifugation. The primary contaminants are aggregates of phage particles and empty capsids. This study then investigates ipDNA conformations by the first cryo-electron microscopy of ipDNA-capsids produced in vivo. The 3-D structures of DNA-free capsids, ipDNA-capsids with various lengths of ipDNA, and mature bacteriophage are reconstructed, which reveals the typical T=7l icosahedral shell of many tailed dsDNA bacteriophages. Though the icosahedral shell structures of these capsids are indistinguishable at the current resolution for the protein shell (approximately 15 A), the conformations of the DNA inside the shell are drastically different. T3 ipDNA-capsids with 10.6 kb or shorter dsDNA (<28% of total genome) have an ipDNA conformation indistinguishable from random. However, T3 ipDNA-capsids with 22 kb DNA (58% of total genome) form a single DNA ring next to the inner surface of the capsid shell. In contrast, dsDNA fully packaged (38.2 kb) in mature T3 phage particles forms multiple concentric rings such as those seen in other tailed dsDNA bacteriophages. The distance between the icosahedral shell and the outermost DNA ring decreases in the mature, fully packaged phage structure. These results suggest that, in the early stage of DNA packaging, the dsDNA genome is randomly distributed inside the capsid, not preferentially packaged against the inner surface of the capsid shell, and that the multiple concentric dsDNA rings seen later are the results of pressure-driven close-packing.","is_dataset_classified":null,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"18952096","pmcid":"PMC2628292","openalex_id":"https://openalex.org/W1990854738","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"GM24365","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"R01 AI072035","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"AI072035","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM024365","title":null}],"total_grants":4,"fwci":2.7234,"citation_percentile":0.88290627,"influential_citations":0,"citation_trend":[{"year":2012,"count":6},{"year":2013,"count":3},{"year":2014,"count":2},{"year":2015,"count":2},{"year":2016,"count":1},{"year":2019,"count":2},{"year":2020,"count":3},{"year":2022,"count":1},{"year":2023,"count":1},{"year":2024,"count":1}],"oa_status":"closed","license":"https://www.elsevier.com/tdm/userlicense/1.0/","oa_locations":[{"url":"https://api.elsevier.com/content/article/PII:S0022283608012849?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0022283608012849?httpAccept=text/plain","host_type":"publisher"},{"url":"https://doi.org/10.1016/j.jmb.2008.10.012","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/18952096","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2628292","host_type":"repository"}],"fields_of_study":["Bacteriophages and microbial interactions","RNA and protein synthesis mechanisms","Advanced Electron Microscopy Techniques and Applications"],"mesh_terms":["Capsid","DNA, Viral","Electrophoresis, Agar Gel","Electrophoresis, Polyacrylamide Gel","Nucleic Acid Denaturation","Mass Spectrometry","Bacteriophage T3","Cryoelectron Microscopy","Protein Structure, Quaternary","Capsid Proteins","DNA Packaging"],"keywords":["Capsid","DNA","Bacteriophage","Icosahedral symmetry","Cryo-electron microscopy","Gel electrophoresis","Biophysics","Centrifugation","Electron microscope","Chemistry","Resolution (logic)","Electrophoresis","Molecular biology","Crystallography","Biology","Escherichia coli","Chromatography","Physics","Biochemistry","Optics","Gene"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-03T04:53:14.623668Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}