PMC:7443692 / 48615-50316 JSONTXT

Annnotations TAB JSON ListView MergeView

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7443692","sourcedb":"PMC","sourceid":"7443692","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7443692","text":"To express a stabilized ectodomain of Spike protein, a synthetic gene encoding residues 1−1208 of SARS-CoV-2 Spike with the furin cleavage site (residues 682–685) replaced by a “GGSG” sequence, proline substitutions at residues 986 and 987, and a foldon trimerization motif followed by a C-terminal 6xHisTag was created and cloned into the mammalian expression vector pCMV-IRES-puro (Codex BioSolutions, Inc, Gaithersburg, MD). The expression construct was transiently transfected in HEK293F cells using polyethylenimine (Polysciences, Inc, Warrington, PA). Protein was purified from cell supernatants using Ni-NTA resin (QIAGEN, Germany), the eluted fractions containing S protein were pooled, concentrated, and further purified by gel filtration chromatography on a Superose 6 column (GE Healthcare). Negative stain electron microscopy (EM) analysis was performed as described (Shaik et al., 2019). Briefly, analysis was performed at room temperature with a magnification of 52,000x and a defocus value of 1.5 μm following low-dose procedures, using a Philips Tecnai F20 electron microscope (Thermo Fisher Scientific) equipped with a Gatan US4000 CCD camera and operated at voltage of 200 kV. The DNA fragment encoding human ACE2 (1-615) with a 6xHis tag at C terminus was synthesized by Genscript and cloned to the vector pCMV-IRES-puro. The expression construct was transfected in HEK293F cells using polyethylenimine. The medium was discarded and replaced with FreeStyle 293 medium after 6-8 h. After incubation in 37°C with 5.5% CO2 for 5 days, the supernatant was collected and loaded to Ni-NTA resin for purification. The elution was concentrated and further purified by a Superdex 200 column.","tracks":[{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T261","span":{"begin":44,"end":51},"obj":"Chemical"},{"id":"T262","span":{"begin":194,"end":201},"obj":"Chemical"},{"id":"T264","span":{"begin":558,"end":565},"obj":"Chemical"},{"id":"T265","span":{"begin":611,"end":614},"obj":"Chemical"},{"id":"T267","span":{"begin":674,"end":681},"obj":"Chemical"},{"id":"T268","span":{"begin":1199,"end":1202},"obj":"Chemical"},{"id":"T269","span":{"begin":1535,"end":1538},"obj":"Chemical"},{"id":"T270","span":{"begin":1598,"end":1601},"obj":"Chemical"}],"attributes":[{"id":"A268","pred":"chebi_id","subj":"T268","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A261","pred":"chebi_id","subj":"T261","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A262","pred":"chebi_id","subj":"T262","obj":"http://purl.obolibrary.org/obo/CHEBI_17203"},{"id":"A263","pred":"chebi_id","subj":"T262","obj":"http://purl.obolibrary.org/obo/CHEBI_26271"},{"id":"A267","pred":"chebi_id","subj":"T267","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A270","pred":"chebi_id","subj":"T270","obj":"http://purl.obolibrary.org/obo/CHEBI_39054"},{"id":"A271","pred":"chebi_id","subj":"T270","obj":"http://purl.obolibrary.org/obo/CHEBI_44557"},{"id":"A264","pred":"chebi_id","subj":"T264","obj":"http://purl.obolibrary.org/obo/CHEBI_16541"},{"id":"A265","pred":"chebi_id","subj":"T265","obj":"http://purl.obolibrary.org/obo/CHEBI_39054"},{"id":"A266","pred":"chebi_id","subj":"T265","obj":"http://purl.obolibrary.org/obo/CHEBI_44557"},{"id":"A269","pred":"chebi_id","subj":"T269","obj":"http://purl.obolibrary.org/obo/CHEBI_16526"},{"subj":"T261","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T262","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T264","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T265","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T267","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T268","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T269","pred":"source","obj":"LitCovid-sample-CHEBI"},{"subj":"T270","pred":"source","obj":"LitCovid-sample-CHEBI"}]},{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T135","span":{"begin":55,"end":69},"obj":"Species"},{"id":"T136","span":{"begin":98,"end":108},"obj":"Species"},{"id":"T137","span":{"begin":350,"end":367},"obj":"Species"},{"id":"T138","span":{"begin":1101,"end":1107},"obj":"Species"},{"id":"T139","span":{"begin":1153,"end":1159},"obj":"Species"},{"id":"T140","span":{"begin":1221,"end":1226},"obj":"Species"}],"attributes":[{"id":"A136","pred":"ncbi_taxonomy_id","subj":"T136","obj":"NCBItxid:2697049"},{"id":"A135","pred":"ncbi_taxonomy_id","subj":"T135","obj":"NCBItxid:2005392"},{"id":"A139","pred":"ncbi_taxonomy_id","subj":"T139","obj":"NCBItxid:274080"},{"id":"A138","pred":"ncbi_taxonomy_id","subj":"T138","obj":"NCBItxid:76720"},{"id":"A137","pred":"ncbi_taxonomy_id","subj":"T137","obj":"NCBItxid:81076"},{"id":"A140","pred":"ncbi_taxonomy_id","subj":"T140","obj":"NCBItxid:9606"},{"subj":"T135","pred":"source","obj":"LitCovid-sample-PD-NCBITaxon"},{"subj":"T136","pred":"source","obj":"LitCovid-sample-PD-NCBITaxon"},{"subj":"T137","pred":"source","obj":"LitCovid-sample-PD-NCBITaxon"},{"subj":"T138","pred":"source","obj":"LitCovid-sample-PD-NCBITaxon"},{"subj":"T139","pred":"source","obj":"LitCovid-sample-PD-NCBITaxon"},{"subj":"T140","pred":"source","obj":"LitCovid-sample-PD-NCBITaxon"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}]},{"project":"LitCovid-sample-sentences","denotations":[{"id":"T332","span":{"begin":0,"end":427},"obj":"Sentence"},{"id":"T333","span":{"begin":428,"end":557},"obj":"Sentence"},{"id":"T334","span":{"begin":558,"end":802},"obj":"Sentence"},{"id":"T335","span":{"begin":803,"end":900},"obj":"Sentence"},{"id":"T336","span":{"begin":901,"end":1194},"obj":"Sentence"},{"id":"T337","span":{"begin":1195,"end":1340},"obj":"Sentence"},{"id":"T338","span":{"begin":1341,"end":1422},"obj":"Sentence"},{"id":"T339","span":{"begin":1423,"end":1499},"obj":"Sentence"},{"id":"T340","span":{"begin":1500,"end":1625},"obj":"Sentence"},{"id":"T341","span":{"begin":1626,"end":1701},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T332","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T333","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T334","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T335","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T336","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T337","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T338","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T339","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T340","pred":"source","obj":"LitCovid-sample-sentences"},{"subj":"T341","pred":"source","obj":"LitCovid-sample-sentences"}]},{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T84","span":{"begin":98,"end":108},"obj":"Disease"}],"attributes":[{"id":"A84","pred":"mondo_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"subj":"T84","pred":"source","obj":"LitCovid-sample-PD-MONDO"}]},{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T3545","span":{"begin":38,"end":51},"obj":"Protein"},{"id":"T3546","span":{"begin":124,"end":129},"obj":"Protein"},{"id":"T3554","span":{"begin":672,"end":681},"obj":"Protein"},{"id":"T3587","span":{"begin":1227,"end":1231},"obj":"Protein"}],"attributes":[{"id":"A3545","pred":"uniprot_id","subj":"T3545","obj":"https://www.uniprot.org/uniprot/P31340"},{"id":"A3546","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/Q9UCZ5"},{"id":"A3547","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/Q6LBS3"},{"id":"A3548","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/Q6GTN6"},{"id":"A3549","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/Q28193"},{"id":"A3550","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/Q14336"},{"id":"A3551","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/P23377"},{"id":"A3552","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/P23188"},{"id":"A3553","pred":"uniprot_id","subj":"T3546","obj":"https://www.uniprot.org/uniprot/P09958"},{"id":"A3554","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9UIP0"},{"id":"A3555","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9UIN9"},{"id":"A3556","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9UIN8"},{"id":"A3557","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9UIN7"},{"id":"A3558","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9UIN6"},{"id":"A3559","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9UBH8"},{"id":"A3560","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NRH8"},{"id":"A3561","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NRH7"},{"id":"A3562","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NRH6"},{"id":"A3563","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NRH5"},{"id":"A3564","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NRH4"},{"id":"A3565","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NPG5"},{"id":"A3566","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NPE0"},{"id":"A3567","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q9NP52"},{"id":"A3568","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q95IF9"},{"id":"A3569","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q8N5P3"},{"id":"A3570","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q8IZU6"},{"id":"A3571","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q8IZU5"},{"id":"A3572","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q8IZU4"},{"id":"A3573","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q86Z04"},{"id":"A3574","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q7YR44"},{"id":"A3575","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q7LA71"},{"id":"A3576","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q7LA70"},{"id":"A3577","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q5STD2"},{"id":"A3578","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q5SQ85"},{"id":"A3579","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q1XI16"},{"id":"A3580","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q1XI12"},{"id":"A3581","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/Q15517"},{"id":"A3582","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/O43509"},{"id":"A3583","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/O19084"},{"id":"A3584","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/B0UYZ7"},{"id":"A3585","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/B0S7V2"},{"id":"A3586","pred":"uniprot_id","subj":"T3554","obj":"https://www.uniprot.org/uniprot/A5A6L9"},{"id":"A3587","pred":"uniprot_id","subj":"T3587","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"subj":"T3545","pred":"source","obj":"LitCovid-sample-UniProt"},{"subj":"T3546","pred":"source","obj":"LitCovid-sample-UniProt"},{"subj":"T3554","pred":"source","obj":"LitCovid-sample-UniProt"},{"subj":"T3587","pred":"source","obj":"LitCovid-sample-UniProt"}]},{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T150","span":{"begin":139,"end":143},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T151","span":{"begin":492,"end":497},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T152","span":{"begin":584,"end":588},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T153","span":{"begin":1393,"end":1398},"obj":"http://purl.obolibrary.org/obo/CL_0000000"}],"attributes":[{"subj":"T150","pred":"source","obj":"LitCovid-sample-PD-IDO"},{"subj":"T151","pred":"source","obj":"LitCovid-sample-PD-IDO"},{"subj":"T152","pred":"source","obj":"LitCovid-sample-PD-IDO"},{"subj":"T153","pred":"source","obj":"LitCovid-sample-PD-IDO"}]},{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T148","span":{"begin":44,"end":51},"obj":"Body_part"},{"id":"T149","span":{"begin":65,"end":69},"obj":"Body_part"},{"id":"T150","span":{"begin":194,"end":201},"obj":"Body_part"},{"id":"T151","span":{"begin":492,"end":497},"obj":"Body_part"},{"id":"T152","span":{"begin":558,"end":565},"obj":"Body_part"},{"id":"T153","span":{"begin":584,"end":588},"obj":"Body_part"},{"id":"T154","span":{"begin":674,"end":681},"obj":"Body_part"},{"id":"T155","span":{"begin":1199,"end":1202},"obj":"Body_part"},{"id":"T156","span":{"begin":1393,"end":1398},"obj":"Body_part"}],"attributes":[{"id":"A153","pred":"fma_id","subj":"T153","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A150","pred":"fma_id","subj":"T150","obj":"http://purl.org/sig/ont/fma/fma82761"},{"id":"A154","pred":"fma_id","subj":"T154","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A149","pred":"fma_id","subj":"T149","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A151","pred":"fma_id","subj":"T151","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A148","pred":"fma_id","subj":"T148","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A156","pred":"fma_id","subj":"T156","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A152","pred":"fma_id","subj":"T152","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A155","pred":"fma_id","subj":"T155","obj":"http://purl.org/sig/ont/fma/fma74412"},{"subj":"T148","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T149","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T150","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T151","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T152","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T153","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T154","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T155","pred":"source","obj":"LitCovid-sample-PD-FMA"},{"subj":"T156","pred":"source","obj":"LitCovid-sample-PD-FMA"}]},{"project":"2_test","denotations":[{"id":"32841605-30542158-19659550","span":{"begin":894,"end":898},"obj":"30542158"}],"attributes":[{"subj":"32841605-30542158-19659550","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-sample-CHEBI","color":"#eca493","default":true},{"id":"LitCovid-sample-PD-NCBITaxon","color":"#939cec"},{"id":"LitCovid-sample-sentences","color":"#b6ec93"},{"id":"LitCovid-sample-PD-MONDO","color":"#ec93d0"},{"id":"LitCovid-sample-UniProt","color":"#93eaec"},{"id":"LitCovid-sample-PD-IDO","color":"#ecd493"},{"id":"LitCovid-sample-PD-FMA","color":"#ba93ec"},{"id":"2_test","color":"#93eca0"}]}]}}