{"id":"https://openalex.org/W2043129552","doi":"https://doi.org/10.1074/jbc.m114.550046","title":"Dissection of the Adenoviral VA RNAI Central Domain Structure Reveals Minimum Requirements for RNA-mediated Inhibition of PKR","display_name":"Dissection of the Adenoviral VA RNAI Central Domain Structure Reveals Minimum Requirements for RNA-mediated Inhibition of PKR","publication_year":2014,"publication_date":"2014-06-27","ids":{"openalex":"https://openalex.org/W2043129552","doi":"https://doi.org/10.1074/jbc.m114.550046","mag":"2043129552","pmid":"https://pubmed.ncbi.nlm.nih.gov/24970889","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4132820"},"language":"en","primary_location":{"id":"doi:10.1074/jbc.m114.550046","doi":"https://doi.org/10.1074/jbc.m114.550046","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m114.550046","pdf_url":null,"source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1074/jbc.m114.550046","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048260033","display_name":"Jo L. Wilson","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jo L. Wilson","raw_affiliation_strings":["Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031607431","display_name":"Virginia K. Vachon","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Virginia K. Vachon","raw_affiliation_strings":["Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102777238","display_name":"S. C. Sunita","orcid":"https://orcid.org/0000-0002-0858-9193","observed_orcids":["https://orcid.org/0000-0002-0858-9193"]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Sunita","raw_affiliation_strings":["Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077744870","display_name":"Samantha L. Schwartz","orcid":"https://orcid.org/0000-0002-3378-0184","observed_orcids":["https://orcid.org/0000-0002-3378-0184"]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samantha L. Schwartz","raw_affiliation_strings":["Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073697186","display_name":"Graeme L. Conn","orcid":"https://orcid.org/0000-0002-2419-380X","observed_orcids":["https://orcid.org/0000-0002-2419-380X"]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Graeme L. Conn","raw_affiliation_strings":["Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322. Electronic address: gconn@emory.edu","Department of Biochemistry; Emory University School of Medicine; Atlanta Georgia 30322"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322. Electronic address: gconn@emory.edu","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Biochemistry; Emory University School of Medicine; Atlanta Georgia 30322","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073697186"],"corresponding_institution_ids":["https://openalex.org/I150468666"],"apc_list":{"value":3430,"currency":"USD","value_usd":3430},"apc_paid":{"value":3430,"currency":"USD","value_usd":3430},"fwci":0.7609,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.70180829,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"289","issue":"33","first_page":"23233","last_page":"23245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.4341000020503998,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.4341000020503998,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.26030001044273376,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":0.08699999749660492,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/adenovirus","display_name":"adenovirus","score":0.8569999933242798},{"id":"https://openalex.org/keywords/pkr","display_name":"PKR","score":0.6930000185966492},{"id":"https://openalex.org/keywords/double-stranded-rna-dependent-protein-kinase","display_name":"double-stranded RNA-dependent protein kinase","score":0.9079999923706055},{"id":"https://openalex.org/keywords/rna-tertiary-structure","display_name":"RNA tertiary structure","score":0.7459999918937683},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"pseudoknot","score":0.9700000286102295},{"id":"https://openalex.org/keywords/innate-immune-evasion","display_name":"innate immune evasion","score":0.6930000185966492},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"non-coding RNA","score":0.7089999914169312},{"id":"https://openalex.org/keywords/ph-dependent-structure","display_name":"pH-dependent structure","score":0.5339999794960022}],"concepts":[{"id":"https://openalex.org/C161238802","wikidata":"https://www.wikidata.org/wiki/Q14905690","display_name":"Protein kinase R","level":5,"score":0.9057723879814148},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.7964754104614258},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7120124101638794},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.6942129731178284},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6302918791770935},{"id":"https://openalex.org/C2777479484","wikidata":"https://www.wikidata.org/wiki/Q5323131","display_name":"EIF-2 kinase","level":5,"score":0.6079136729240417},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.46646368503570557},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3130185306072235},{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.27676382660865784},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26251140236854553},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.2587999105453491},{"id":"https://openalex.org/C90934575","wikidata":"https://www.wikidata.org/wiki/Q6593810","display_name":"Mitogen-activated protein kinase kinase","level":4,"score":0.0},{"id":"https://openalex.org/C82495950","wikidata":"https://www.wikidata.org/wiki/Q14911732","display_name":"Cyclin-dependent kinase 2","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000256","descriptor_name":"Adenoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000256","descriptor_name":"Adenoviridae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000256","descriptor_name":"Adenoviridae","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008274","descriptor_name":"Magnesium","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019892","descriptor_name":"eIF-2 Kinase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D019892","descriptor_name":"eIF-2 Kinase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019892","descriptor_name":"eIF-2 Kinase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019892","descriptor_name":"eIF-2 Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1074/jbc.m114.550046","doi":"https://doi.org/10.1074/jbc.m114.550046","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m114.550046","pdf_url":null,"source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4132820","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4132820","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Biol Chem","raw_type":"Text"},{"id":"pmid:24970889","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24970889","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of biological chemistry","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1074/jbc.m114.550046","doi":"https://doi.org/10.1074/jbc.m114.550046","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m114.550046","pdf_url":null,"source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G4385957735","display_name":"Structural studies of PKR regulation by viral non-coding RNA","funder_award_id":"R21AI097803","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W331688924","https://openalex.org/W1510178633","https://openalex.org/W1567874198","https://openalex.org/W1804987977","https://openalex.org/W1963847212","https://openalex.org/W1972533328","https://openalex.org/W1972600692","https://openalex.org/W1973179284","https://openalex.org/W1974033281","https://openalex.org/W1990810479","https://openalex.org/W2006273686","https://openalex.org/W2027131183","https://openalex.org/W2030117043","https://openalex.org/W2035266502","https://openalex.org/W2053312233","https://openalex.org/W2060167034","https://openalex.org/W2060419010","https://openalex.org/W2063116879","https://openalex.org/W2065043474","https://openalex.org/W2067485395","https://openalex.org/W2076846676","https://openalex.org/W2077838722","https://openalex.org/W2078339163","https://openalex.org/W2098472306","https://openalex.org/W2105032204","https://openalex.org/W2106478835","https://openalex.org/W2108736984","https://openalex.org/W2118553480","https://openalex.org/W2120974004","https://openalex.org/W2131575287","https://openalex.org/W2135417411","https://openalex.org/W2140726238","https://openalex.org/W2140973201","https://openalex.org/W2141556611","https://openalex.org/W2141827362","https://openalex.org/W2151073330","https://openalex.org/W2157748846","https://openalex.org/W2160528720","https://openalex.org/W2166329605","https://openalex.org/W2170284780","https://openalex.org/W2400352781","https://openalex.org/W6683566087"],"related_works":["https://openalex.org/W7098784387","https://openalex.org/W1510178633","https://openalex.org/W2165865737","https://openalex.org/W2001562342","https://openalex.org/W174923191","https://openalex.org/W2078339163","https://openalex.org/W2170284780","https://openalex.org/W2103538081","https://openalex.org/W1987753497","https://openalex.org/W2160528720"],"abstract_inverted_index":{"Virus-associated":[0],"RNA":[1,10,194],"I":[2],"(VA":[3],"RNAI)":[4],"is":[5,33],"a":[6,37,53,85,116,127],"short":[7],"(\u223c160-nucleotide)":[8],"non-coding":[9],"transcript":[11],"employed":[12],"by":[13,161],"adenoviruses":[14],"to":[15,35,43,69,102,158,165],"subvert":[16],"the":[17,82,95,123,138,142,147,170,189],"innate":[18],"immune":[19],"system":[20],"protein":[21,24],"double-stranded":[22],"RNA-activated":[23],"kinase":[25],"(PKR).":[26],"The":[27],"central":[28,96,112,143,148],"domain":[29,113,149],"of":[30,55,84,111,141,146,179,196],"VA":[31,56,180],"RNAI":[32,57,181],"proposed":[34],"contain":[36],"complex":[38],"tertiary":[39,72,89,124],"structure":[40,73,90,100,125],"that":[41,188],"contributes":[42],"its":[44,76,163],"optimal":[45],"inhibitory":[46],"activity":[47,65,155],"against":[48],"PKR.":[49],"Here":[50],"we":[51],"use":[52],"combination":[54],"mutagenesis,":[58],"structural":[59],"analyses,":[60],"as":[61,63],"well":[62],"PKR":[64,108,131,184,197],"and":[66,74,87,133,186],"binding":[67,132],"assays":[68],"dissect":[70],"this":[71,99],"assess":[75],"functional":[77],"role.":[78],"Our":[79],"results":[80,176],"support":[81],"existence":[83],"pH-":[86],"Mg(2+)-dependent":[88],"involving":[91],"pseudoknot":[92],"formation":[93],"within":[94,115],"domain.":[97,144],"Unexpectedly,":[98],"appears":[101,157],"play":[103],"no":[104],"direct":[105],"role":[106,129],"in":[107,130,137,167],"inhibition.":[109],"Deletion":[110,145],"sequences":[114],"minimal":[117],"but":[118,156],"fully":[119],"active":[120],"construct":[121],"lacking":[122],"reveals":[126],"crucial":[128],"inhibition":[134,185],"for":[135,183,191],"nucleotides":[136],"5'":[139,171],"half":[140,151,172],"3'":[150],"also":[152],"significantly":[153],"impacts":[154],"arise":[159],"indirectly":[160],"reducing":[162],"capacity":[164],"assist":[166],"optimally":[168],"presenting":[169],"sequence.":[173],"Collectively,":[174],"our":[175],"identify":[177],"regions":[178],"critical":[182],"reveal":[187],"requirements":[190],"an":[192],"effective":[193],"inhibitor":[195],"are":[198],"simpler":[199],"than":[200],"appreciated":[201],"previously.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":4}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}