{"id":"https://openalex.org/W2138701247","doi":null,"title":"Structural and Genetic Studies of Translation in Escherichia coli","display_name":"Structural and Genetic Studies of Translation in Escherichia coli","publication_year":2005,"publication_date":"2005-01-01","ids":{"openalex":"https://openalex.org/W2138701247","mag":"2138701247"},"language":"en","primary_location":{"id":"pmh:oai:DiVA.org:su-601","doi":null,"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-601","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-601","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102049759","display_name":"Qing H. Zhao","orcid":"https://orcid.org/0000-0001-7277-9066","observed_orcids":["https://orcid.org/0000-0001-7277-9066"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Qing Zhao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5102049759"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T11162","display_name":"Enzyme Structure and Function","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/translation-biology","display_name":"translation (biology)","score":0.4620000123977661},{"id":"https://openalex.org/keywords/ribosome-structure","display_name":"ribosome structure","score":0.8130000233650208},{"id":"https://openalex.org/keywords/30s-ribosomal-subunit","display_name":"30S ribosomal subunit","score":0.9179999828338623},{"id":"https://openalex.org/keywords/50s-ribosomal-subunit","display_name":"50S ribosomal subunit","score":0.9990000128746033},{"id":"https://openalex.org/keywords/conformational-flexibility","display_name":"conformational flexibility","score":0.871999979019165},{"id":"https://openalex.org/keywords/cryo-electron-tomography","display_name":"cryo-electron tomography","score":0.8420000076293945},{"id":"https://openalex.org/keywords/peptidyl-transferase-center","display_name":"peptidyl transferase center","score":0.8759999871253967},{"id":"https://openalex.org/keywords/translation-initiation","display_name":"translation initiation","score":0.6179999709129333},{"id":"https://openalex.org/keywords/shine-dalgarno-sequence","display_name":"Shine-Dalgarno sequence","score":0.9940000176429749},{"id":"https://openalex.org/keywords/anti-shine-dalgarno-sequence","display_name":"anti-Shine-Dalgarno sequence","score":0.8690000176429749},{"id":"https://openalex.org/keywords/16s-rrna","display_name":"16S rRNA","score":0.8489999771118164},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.824999988079071}],"concepts":[{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.686553955078125},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5523107647895813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.373868465423584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34848058223724365},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3234274983406067},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17638325691223145},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:DiVA.org:su-601","doi":null,"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-601","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},{"id":"mag:2138701247","doi":null,"is_oa":false,"landing_page_url":"http://su.diva-portal.org/smash/record.jsf?pid=diva2:195925","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:DiVA.org:su-601","doi":null,"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-601","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":161,"referenced_works":["https://openalex.org/W12346750","https://openalex.org/W140176686","https://openalex.org/W202607681","https://openalex.org/W217156697","https://openalex.org/W1514366116","https://openalex.org/W1554349566","https://openalex.org/W1556526714","https://openalex.org/W1561858598","https://openalex.org/W1575999626","https://openalex.org/W1576552863","https://openalex.org/W1586232998","https://openalex.org/W1605208286","https://openalex.org/W1654771893","https://openalex.org/W1870805240","https://openalex.org/W1965198018","https://openalex.org/W1965252702","https://openalex.org/W1965257507","https://openalex.org/W1966074306","https://openalex.org/W1966301130","https://openalex.org/W1966473942","https://openalex.org/W1969156185","https://openalex.org/W1972706642","https://openalex.org/W1975924299","https://openalex.org/W1977233639","https://openalex.org/W1980653793","https://openalex.org/W1981020015","https://openalex.org/W1983534198","https://openalex.org/W1983593096","https://openalex.org/W1989794771","https://openalex.org/W1991890337","https://openalex.org/W1992226159","https://openalex.org/W1992481862","https://openalex.org/W1995785876","https://openalex.org/W1996632741","https://openalex.org/W1996652228","https://openalex.org/W2000219748","https://openalex.org/W2000224326","https://openalex.org/W2000483347","https://openalex.org/W2000915984","https://openalex.org/W2002859668","https://openalex.org/W2005601437","https://openalex.org/W2005843451","https://openalex.org/W2006243507","https://openalex.org/W2006923455","https://openalex.org/W2007369397","https://openalex.org/W2007890475","https://openalex.org/W2008929657","https://openalex.org/W2010972197","https://openalex.org/W2011038859","https://openalex.org/W2012879790","https://openalex.org/W2016412131","https://openalex.org/W2016755680","https://openalex.org/W2018664851","https://openalex.org/W2018668138","https://openalex.org/W2019301374","https://openalex.org/W2020222936","https://openalex.org/W2020302409","https://openalex.org/W2020346411","https://openalex.org/W2021761289","https://openalex.org/W2021901075","https://openalex.org/W2024684906","https://openalex.org/W2026019425","https://openalex.org/W2027262380","https://openalex.org/W2029132648","https://openalex.org/W2030405536","https://openalex.org/W2032191472","https://openalex.org/W2034304629","https://openalex.org/W2034743409","https://openalex.org/W2036032941","https://openalex.org/W2037129989","https://openalex.org/W2037213262","https://openalex.org/W2037832052","https://openalex.org/W2039306826","https://openalex.org/W2039691170","https://openalex.org/W2041913199","https://openalex.org/W2045690036","https://openalex.org/W2046938811","https://openalex.org/W2048904456","https://openalex.org/W2050463607","https://openalex.org/W2052163946","https://openalex.org/W2058426472","https://openalex.org/W2060419010","https://openalex.org/W2061146689","https://openalex.org/W2062390525","https://openalex.org/W2063016599","https://openalex.org/W2063372773","https://openalex.org/W2063756267","https://openalex.org/W2064398741","https://openalex.org/W2066010536","https://openalex.org/W2066254905","https://openalex.org/W2067187070","https://openalex.org/W2070165671","https://openalex.org/W2071043117","https://openalex.org/W2071390057","https://openalex.org/W2071804506","https://openalex.org/W2071840045","https://openalex.org/W2073354904","https://openalex.org/W2077105547","https://openalex.org/W2077580539","https://openalex.org/W2082138488","https://openalex.org/W2084124582","https://openalex.org/W2085211780","https://openalex.org/W2086830419","https://openalex.org/W2087679230","https://openalex.org/W2088230790","https://openalex.org/W2089704642","https://openalex.org/W2091336733","https://openalex.org/W2092089208","https://openalex.org/W2092617311","https://openalex.org/W2093062181","https://openalex.org/W2093253527","https://openalex.org/W2093471887","https://openalex.org/W2094333855","https://openalex.org/W2094869942","https://openalex.org/W2097225375","https://openalex.org/W2097654784","https://openalex.org/W2100882223","https://openalex.org/W2101399358","https://openalex.org/W2101918141","https://openalex.org/W2104482488","https://openalex.org/W2109245000","https://openalex.org/W2110267171","https://openalex.org/W2110810808","https://openalex.org/W2112130400","https://openalex.org/W2113761741","https://openalex.org/W2116243772","https://openalex.org/W2116541947","https://openalex.org/W2116611793","https://openalex.org/W2117808511","https://openalex.org/W2119966574","https://openalex.org/W2120498503","https://openalex.org/W2121871801","https://openalex.org/W2123625319","https://openalex.org/W2124433456","https://openalex.org/W2125917944","https://openalex.org/W2126780661","https://openalex.org/W2128167475","https://openalex.org/W2128488575","https://openalex.org/W2129561341","https://openalex.org/W2134153749","https://openalex.org/W2134660959","https://openalex.org/W2137457846","https://openalex.org/W2137473984","https://openalex.org/W2138840910","https://openalex.org/W2142731338","https://openalex.org/W2145583354","https://openalex.org/W2148083213","https://openalex.org/W2149357806","https://openalex.org/W2155153804","https://openalex.org/W2158023121","https://openalex.org/W2158157849","https://openalex.org/W2161120281","https://openalex.org/W2162522101","https://openalex.org/W2162584369","https://openalex.org/W2163076661","https://openalex.org/W2167358474","https://openalex.org/W2168580817","https://openalex.org/W2168640133","https://openalex.org/W2170243611","https://openalex.org/W2170602689","https://openalex.org/W2395549144"],"related_works":["https://openalex.org/W2027262380","https://openalex.org/W2064398741","https://openalex.org/W2066644842","https://openalex.org/W78066905","https://openalex.org/W7095117629","https://openalex.org/W2025641516","https://openalex.org/W947988062","https://openalex.org/W2134027771","https://openalex.org/W1986983983","https://openalex.org/W1533190207"],"abstract_inverted_index":{"Ribosomes":[0],"are":[1,20,135,187],"the":[2,8,17,29,49,54,58,73,87,115,118,120,123,143,163,167,170,173,176,181,188,195,205,208,212,222,267,271,282,300,310,315,369,380,386,393,414,422,452,457],"universal":[3],"ribonucleoprotein":[4],"organelles":[5],"that":[6,71,421,429],"translate":[7],"genetic":[9,59],"message":[10],"from":[11,445],"mRNA":[12,283,453],"to":[13,95,130,142,159,287,309,431,441,447],"protein.":[14,62],"In":[15,114,166,225],"prokaryotes,":[16],"ribosomal":[18,246,449],"subunits":[19,102,111,216],"30S":[21,101,116,164],"and":[22,42,105,108,122,180,191,251,262,270,385,413],"50S":[23,110,168,215],"subunit,":[24,117,169],"which":[25],"bind":[26,430],"together":[27],"during":[28],"translation":[30,277,289,304],"process":[31,55,258],"forming":[32],"70S":[33],"ribosome.":[34],"The":[35,133,291,338,373,418],"ribosome":[36],"is":[37,66,255,266,345,357,377,389,397,401,408,454],"a":[38,45,83,156,218,240,404],"highly":[39,273],"dynamic":[40,190],"structure,":[41],"acts":[43],"as":[44,155],"working":[46],"platform":[47,121],"for":[48,259,427],"different":[50],"factors":[51],"involved":[52],"in":[53,103,106,112,162,194,207,213,234,249,252],"of":[56,75,86,204,276,299,334,341,459,472],"converting":[57],"information":[60],"into":[61,137],"Cryo-electron":[63],"tomography":[64],"(cryo-ET)":[65],"an":[67,147,256,323,335,342,355,432],"emerging":[68],"imaging":[69],"technology":[70],"combines":[72],"potential":[74,361],"three-dimensional":[76],"(3D)":[77],"reconstruction":[78],"at":[79,368],"molecular":[80],"resolution":[81],"with":[82,198],"close-to-native":[84],"preservation":[85],"specimen.":[88],"Here,":[89],"we":[90],"have":[91,284,319],"applied":[92],"this":[93,383,411,469],"method":[94],"reconstruct":[96],"rifampicin-treated":[97],"Escherichia":[98],"coli":[99],"individual":[100,109,245],"vitro":[104,250],"situ,":[107],"situ.":[113,253],"head,":[119],"body":[124],"show":[125],"large":[126,223],"conformational":[127,139,242],"movements":[128,200],"relative":[129],"each":[131],"other.":[132],"particles":[134],"grouped":[136],"three":[138],"groups":[140],"according":[141],"width/height":[144],"ratios.":[145],"Also,":[146],"S15":[148,161],"fusion":[149],"protein":[150],"derivative":[151],"has":[152],"been":[153,232,285],"used":[154],"physical":[157],"reporter":[158],"localize":[160],"subunit.":[165,224],"L1":[171],"stalk,":[172,175],"L7/L12":[174],"central":[177,209],"protuberance":[178],"(CP),":[179],"peptidyl":[182],"transferase":[183],"center":[184],"(PTC)":[185],"cleft":[186],"most":[189,272],"flexible":[192,219],"parts":[193],"reconstructed":[196],"structures":[197],"clear":[199],"indicated.":[201],"Different":[202],"locations":[203],"tunnel":[206],"cross-sections":[210],"through":[211],"situ":[214],"indicate":[217],"pathway":[220],"inside":[221],"addition,":[226],"gross":[227],"morphological":[228],"changes":[229],"were":[230],"also":[231],"observed":[233],"our":[235],"reconstructions.":[236],"Our":[237],"results":[238,419],"demonstrate":[239],"considerable":[241],"flexibility":[243],"among":[244],"subunits,":[247],"both":[248],"Translation":[254,264],"essential":[257],"all":[260],"cells":[261],"organisms.":[263],"initiation":[265,301,305,336,362,364,400,443],"rate-limiting":[268],"step":[269],"regulated":[274],"phase":[275],"process.":[278],"Several":[279],"regions":[280],"along":[281,451],"reported":[286],"influence":[288,466],"initiation.":[290],"Shine-Dalgarno":[292],"(SD)":[293],"sequence":[294,313,325],"located":[295,330,434],"5-9":[296],"bases":[297],"upstream":[298,331,343,415,442],"codon":[302],"supports":[303],"by":[306],"complementary":[307],"binding":[308],"Anti-Shine-Dalgarno":[311],"(ASD)":[312],"on":[314],"16S":[316],"rRNA.":[317],"We":[318],"here":[320],"compared":[321],"how":[322],"SD+":[324,344,349,356,388,412,433,460],"influences":[326],"gene":[327,352,467],"expression,":[328,468],"if":[329,379,392,403],"or":[332,461],"downstream":[333,348,387],"codon.":[337],"positive":[339,439],"effect":[340],"confirmed.":[346],"A":[347,437],"gives":[350],"decreased":[351],"expression.":[353],"If":[354],"placed":[358,409],"between":[359,382,410,435],"two":[360,423],"codons,":[363],"takes":[365],"place":[366],"predominantly":[367],"second":[370,394],"start":[371,375,395,416,424],"site.":[372,417],"first":[374],"site":[376,384,396],"activated":[378],"distance":[381],"enlarged":[390],"and/or":[391],"weakened.":[398],"Upstream":[399],"eliminated":[402],"stable":[405],"stem-loop":[406],"structure":[407],"suggest":[420],"sites":[425],"compete":[426],"ribosomes":[428],"them.":[436],"minor":[438],"contribution":[440],"resulting":[444],"3\u2019":[446],"5\u2019":[448],"diffusion":[450],"suggested.":[455],"Since":[456],"location":[458],"SD-like":[462],"sequences":[463],"can":[464],"strongly":[465],"should":[470],"be":[471],"significant":[473],"evolutionary":[474],"importance.":[475]},"counts_by_year":[],"updated_date":"2026-10-03T13:16:28.481748","created_date":"2016-06-24T00:00:00"}