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PMC:7199903 / 4170-5314 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T26 63-70 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 127-134 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 441-448 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T29 493-500 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 998-1005 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T22 50-58 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 480-488 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 898-906 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T33 367-368 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 462-464 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T35 643-644 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 735-736 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 1037-1039 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T26 63-70 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T27 127-134 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T28 311-319 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T29 337-339 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T30 441-448 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T31 465-472 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T32 493-500 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T33 651-658 Chemical denotes Gly-Ser http://purl.obolibrary.org/obo/CHEBI_73516
T34 651-654 Chemical denotes Gly http://purl.obolibrary.org/obo/CHEBI_15428
T35 655-658 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T37 659-666 Chemical denotes Ala-Ser http://purl.obolibrary.org/obo/CHEBI_73394
T38 659-662 Chemical denotes Ala http://purl.obolibrary.org/obo/CHEBI_16977|http://purl.obolibrary.org/obo/CHEBI_46217
T40 663-666 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T42 998-1005 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43 1131-1133 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T27 15-19 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T28 187-197 http://purl.obolibrary.org/obo/IDO_0000608 denotes replicates
T29 703-707 http://purl.obolibrary.org/obo/BFO_0000029 denotes site

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T671 0-2 TO denotes To
T672 3-10 VB denotes resolve
T673 11-14 DT denotes the
T674 15-28 JJ denotes site-specific
T675 29-42 NN denotes glycosylation
T676 43-45 IN denotes of
T677 46-49 DT denotes the
T678 50-60 NN denotes SARS-CoV-2
T679 61-62 NN denotes S
T680 63-70 NN denotes protein
T681 71-74 CC denotes and
T682 75-84 VB denotes visualize
T683 85-88 DT denotes the
T684 89-101 NN denotes distribution
T685 102-104 IN denotes of
T686 105-115 NNS denotes glycoforms
T687 116-122 IN denotes across
T688 123-126 DT denotes the
T689 127-134 NN denotes protein
T690 135-142 NN denotes surface
T691 142-143 -COMMA- denotes ,
T692 144-146 PRP denotes we
T693 147-156 VBD denotes expressed
T694 157-160 CC denotes and
T695 161-169 VBN denotes purified
T696 170-175 CD denotes three
T697 176-186 JJ denotes biological
T698 187-197 NNS denotes replicates
T699 198-200 IN denotes of
T700 201-212 JJ denotes recombinant
T701 213-220 JJ denotes soluble
T702 221-229 NN denotes material
T703 230-232 IN denotes in
T704 233-235 DT denotes an
T705 236-245 JJ denotes identical
T706 246-252 NN denotes manner
T707 253-255 TO denotes to
T708 256-260 DT denotes that
T709 261-266 WDT denotes which
T710 267-270 VBD denotes was
T711 271-275 VBN denotes used
T712 276-278 TO denotes to
T713 279-285 VB denotes obtain
T714 286-289 DT denotes the
T715 290-305 JJ denotes high-resolution
T716 306-319 NN denotes cryo–electron
T717 320-330 NN denotes microscopy
T718 331-332 -LRB- denotes (
T719 332-339 NN denotes cryo-EM
T720 339-340 -RRB- denotes )
T721 341-350 NN denotes structure
T722 350-351 -COMMA- denotes ,
T723 352-358 IN denotes albeit
T724 359-366 IN denotes without
T725 367-368 DT denotes a
T726 369-386 NN denotes glycan-processing
T727 387-395 NN denotes blockade
T728 396-401 VBG denotes using
T729 402-413 NN denotes kifunensine
T730 414-415 -LRB- denotes (
T731 415-416 CD denotes 4
T732 416-417 -RRB- denotes )
T733 419-423 DT denotes This
T734 424-431 NN denotes variant
T735 432-434 IN denotes of
T736 435-438 DT denotes the
T737 439-440 NN denotes S
T738 441-448 NN denotes protein
T739 449-457 VBZ denotes contains
T740 458-461 DT denotes all
T741 462-464 CD denotes 22
T742 465-472 NNS denotes glycans
T743 473-475 IN denotes on
T744 476-479 DT denotes the
T745 480-490 NN denotes SARS-CoV-2
T746 491-492 NN denotes S
T747 493-500 NN denotes protein
T748 501-502 -LRB- denotes (
T749 502-506 NN denotes Fig.
T750 507-509 NN denotes 1A
T751 509-510 -RRB- denotes )
T752 512-525 NN denotes Stabilization
T753 526-528 IN denotes of
T754 529-532 DT denotes the
T755 533-541 JJ denotes trimeric
T756 542-551 NN denotes prefusion
T757 552-561 NN denotes structure
T758 562-565 VBD denotes was
T759 566-574 VBN denotes achieved
T760 575-577 IN denotes by
T761 578-583 VBG denotes using
T762 584-587 DT denotes the
T763 588-590 NN denotes 2P
T764 591-602 VBG denotes stabilizing
T765 603-612 NNS denotes mutations
T766 613-614 -LRB- denotes (
T767 614-616 CD denotes 20
T768 616-617 -RRB- denotes )
T769 618-620 IN denotes at
T770 621-629 NNS denotes residues
T771 630-633 CD denotes 986
T772 634-637 CC denotes and
T773 638-641 CD denotes 987
T774 641-642 -COMMA- denotes ,
T775 643-644 DT denotes a
T776 645-649 NN denotes GSAS
T777 650-651 -LRB- denotes (
T778 651-666 NN denotes Gly-Ser-Ala-Ser
T779 666-667 -RRB- denotes )
T780 668-680 NN denotes substitution
T781 681-683 IN denotes at
T782 684-687 DT denotes the
T783 688-693 NN denotes furin
T784 694-702 NN denotes cleavage
T785 703-707 NN denotes site
T786 708-709 -LRB- denotes (
T787 709-717 NNS denotes residues
T788 718-721 CD denotes 682
T789 722-724 TO denotes to
T790 725-728 CD denotes 685
T791 728-729 -RRB- denotes )
T792 729-730 -COMMA- denotes ,
T793 731-734 CC denotes and
T794 735-736 DT denotes a
T795 737-747 JJ denotes C-terminal
T796 748-761 NN denotes trimerization
T797 762-767 NN denotes motif
T798 769-773 DT denotes This
T799 774-779 VBZ denotes helps
T800 780-782 TO denotes to
T801 783-791 VB denotes maintain
T802 792-802 JJ denotes quaternary
T803 803-815 NN denotes architecture
T804 816-822 IN denotes during
T805 823-829 NN denotes glycan
T806 830-840 NN denotes processing
T807 842-848 IN denotes Before
T808 849-857 NN denotes analysis
T809 857-858 -COMMA- denotes ,
T810 859-870 NN denotes supernatant
T811 871-881 VBG denotes containing
T812 882-885 DT denotes the
T813 886-897 JJ denotes recombinant
T814 898-908 NN denotes SARS-CoV-2
T815 909-910 NN denotes S
T816 911-914 VBD denotes was
T817 915-923 VBN denotes purified
T818 924-926 IN denotes by
T819 927-931 NN denotes size
T820 932-941 NN denotes exclusion
T821 942-956 NN denotes chromatography
T822 957-959 TO denotes to
T823 960-966 VB denotes ensure
T824 967-971 IN denotes that
T825 972-976 RB denotes only
T826 977-988 JJ denotes native-like
T827 989-997 JJ denotes trimeric
T828 998-1005 NN denotes protein
T829 1006-1009 VBD denotes was
T830 1010-1018 VBN denotes analyzed
T831 1019-1020 -LRB- denotes (
T832 1020-1024 NNP denotes Fig.
T833 1025-1027 NN denotes 1B
T834 1028-1031 CC denotes and
T835 1032-1035 NN denotes fig
T836 1037-1039 NN denotes S1
T837 1039-1040 -RRB- denotes )
T838 1042-1045 DT denotes The
T839 1046-1054 JJ denotes trimeric
T840 1055-1067 NN denotes conformation
T841 1068-1070 IN denotes of
T842 1071-1074 DT denotes the
T843 1075-1083 VBN denotes purified
T844 1084-1092 NN denotes material
T845 1093-1096 VBD denotes was
T846 1097-1106 VBN denotes validated
T847 1107-1109 IN denotes by
T848 1110-1115 VBG denotes using
T849 1116-1130 JJ denotes negative-stain
T850 1131-1133 NN denotes EM
T851 1134-1135 -LRB- denotes (
T852 1135-1139 NN denotes Fig.
T853 1140-1142 NN denotes 1C
T854 1142-1143 -RRB- denotes )
R729 T711 T724 arg1Of used,without
R730 T727 T724 arg2Of blockade,without
R731 T727 T725 arg1Of blockade,a
R732 T727 T726 arg1Of blockade,glycan-processing
R733 T727 T728 arg1Of blockade,using
R734 T729 T728 arg2Of kifunensine,using
R735 T729 T730 arg1Of kifunensine,(
R736 T731 T730 arg2Of 4,(
R673 T681 T671 arg1Of and,To
R674 T693 T671 modOf expressed,To
R675 T692 T672 arg1Of we,resolve
R676 T675 T672 arg2Of glycosylation,resolve
R677 T675 T673 arg1Of glycosylation,the
R678 T675 T674 arg1Of glycosylation,site-specific
R679 T675 T676 arg1Of glycosylation,of
R680 T680 T676 arg2Of protein,of
R681 T680 T677 arg1Of protein,the
R682 T680 T678 arg1Of protein,SARS-CoV-2
R683 T680 T679 arg1Of protein,S
R684 T672 T681 arg1Of resolve,and
R685 T682 T681 arg2Of visualize,and
R686 T692 T682 arg1Of we,visualize
R687 T684 T682 arg2Of distribution,visualize
R688 T684 T683 arg1Of distribution,the
R689 T684 T685 arg1Of distribution,of
R690 T686 T685 arg2Of glycoforms,of
R691 T684 T687 arg1Of distribution,across
R692 T690 T687 arg2Of surface,across
R693 T690 T688 arg1Of surface,the
R694 T690 T689 arg1Of surface,protein
R695 T693 T691 arg1Of expressed,","
R696 T692 T693 arg1Of we,expressed
R697 T698 T693 arg2Of replicates,expressed
R698 T698 T694 arg1Of replicates,and
R699 T698 T695 arg2Of replicates,purified
R700 T698 T696 arg1Of replicates,three
R701 T698 T697 arg1Of replicates,biological
R702 T698 T699 arg1Of replicates,of
R703 T702 T699 arg2Of material,of
R704 T702 T700 arg1Of material,recombinant
R705 T702 T701 arg1Of material,soluble
R706 T693 T703 arg1Of expressed,in
R707 T706 T703 arg2Of manner,in
R708 T706 T704 arg1Of manner,an
R709 T706 T705 arg1Of manner,identical
R710 T693 T707 arg1Of expressed,to
R711 T708 T707 arg2Of that,to
R712 T708 T709 arg1Of that,which
R713 T708 T710 arg1Of that,was
R714 T711 T710 arg2Of used,was
R715 T708 T711 arg2Of that,used
R716 T713 T711 arg3Of obtain,used
R717 T713 T712 arg1Of obtain,to
R718 T708 T713 arg1Of that,obtain
R719 T721 T713 arg2Of structure,obtain
R720 T721 T714 arg1Of structure,the
R721 T717 T715 arg1Of microscopy,high-resolution
R722 T717 T716 arg1Of microscopy,cryo–electron
R723 T721 T717 arg1Of structure,microscopy
R724 T717 T718 arg1Of microscopy,(
R725 T719 T718 arg2Of cryo-EM,(
R726 T720 T718 arg3Of ),(
R727 T711 T722 arg1Of used,","
R728 T724 T723 arg1Of without,albeit
R737 T732 T730 arg3Of ),(
R738 T734 T733 arg1Of variant,This
R739 T734 T735 arg1Of variant,of
R740 T738 T735 arg2Of protein,of
R741 T738 T736 arg1Of protein,the
R742 T738 T737 arg1Of protein,S
R743 T734 T739 arg1Of variant,contains
R744 T742 T739 arg2Of glycans,contains
R745 T741 T740 arg1Of 22,all
R746 T742 T741 arg1Of glycans,22
R747 T739 T743 arg1Of contains,on
R748 T747 T743 arg2Of protein,on
R749 T747 T744 arg1Of protein,the
R750 T747 T745 arg1Of protein,SARS-CoV-2
R751 T747 T746 arg1Of protein,S
R752 T747 T748 arg1Of protein,(
R753 T750 T748 arg2Of 1A,(
R754 T751 T748 arg3Of ),(
R755 T750 T749 arg1Of 1A,Fig.
R756 T752 T753 arg1Of Stabilization,of
R757 T757 T753 arg2Of structure,of
R758 T757 T754 arg1Of structure,the
R759 T757 T755 arg1Of structure,trimeric
R760 T757 T756 arg1Of structure,prefusion
R761 T752 T758 arg1Of Stabilization,was
R762 T759 T758 arg2Of achieved,was
R763 T752 T759 arg2Of Stabilization,achieved
R764 T759 T760 arg1Of achieved,by
R765 T761 T760 arg2Of using,by
R766 T765 T761 arg2Of mutations,using
R767 T765 T762 arg1Of mutations,the
R768 T765 T763 arg1Of mutations,2P
R769 T765 T764 arg1Of mutations,stabilizing
R770 T765 T766 arg1Of mutations,(
R771 T767 T766 arg2Of 20,(
R772 T768 T766 arg3Of ),(
R773 T761 T769 arg1Of using,at
R774 T793 T769 arg2Of and,at
R775 T772 T770 arg1Of and,residues
R776 T771 T772 arg1Of 986,and
R777 T773 T772 arg2Of 987,and
R778 T772 T774 arg1Of and,","
R779 T780 T774 arg2Of substitution,","
R780 T780 T775 arg1Of substitution,a
R781 T780 T776 arg1Of substitution,GSAS
R782 T780 T777 arg1Of substitution,(
R783 T778 T777 arg2Of Gly-Ser-Ala-Ser,(
R784 T779 T777 arg3Of ),(
R785 T780 T781 arg1Of substitution,at
R786 T785 T781 arg2Of site,at
R787 T785 T782 arg1Of site,the
R788 T785 T783 arg1Of site,furin
R789 T785 T784 arg1Of site,cleavage
R790 T785 T786 arg1Of site,(
R791 T790 T786 arg2Of 685,(
R792 T791 T786 arg3Of ),(
R793 T790 T787 arg1Of 685,residues
R794 T790 T788 arg1Of 685,682
R795 T790 T789 arg1Of 685,to
R796 T793 T792 arg1Of and,","
R797 T772 T793 arg1Of and,and
R798 T797 T793 arg2Of motif,and
R799 T797 T794 arg1Of motif,a
R800 T797 T795 arg1Of motif,C-terminal
R801 T797 T796 arg1Of motif,trimerization
R802 T798 T799 arg1Of This,helps
R803 T801 T799 arg2Of maintain,helps
R804 T801 T800 arg1Of maintain,to
R805 T798 T801 arg1Of This,maintain
R806 T803 T801 arg2Of architecture,maintain
R807 T803 T802 arg1Of architecture,quaternary
R808 T801 T804 arg1Of maintain,during
R809 T806 T804 arg2Of processing,during
R810 T806 T805 arg1Of processing,glycan
R811 T817 T807 arg1Of purified,Before
R812 T808 T807 arg2Of analysis,Before
R813 T817 T809 arg1Of purified,","
R814 T810 T811 arg1Of supernatant,containing
R815 T815 T811 arg2Of S,containing
R816 T815 T812 arg1Of S,the
R817 T815 T813 arg1Of S,recombinant
R818 T815 T814 arg1Of S,SARS-CoV-2
R819 T810 T816 arg1Of supernatant,was
R820 T817 T816 arg2Of purified,was
R821 T821 T817 arg1Of chromatography,purified
R822 T810 T817 arg2Of supernatant,purified
R823 T821 T818 arg2Of chromatography,by
R824 T821 T819 arg1Of chromatography,size
R825 T821 T820 arg1Of chromatography,exclusion
R826 T823 T822 arg1Of ensure,to
R827 T817 T822 modOf purified,to
R828 T810 T823 arg1Of supernatant,ensure
R829 T830 T823 arg2Of analyzed,ensure
R830 T830 T824 arg1Of analyzed,that
R831 T828 T825 arg1Of protein,only
R832 T828 T826 arg1Of protein,native-like
R833 T828 T827 arg1Of protein,trimeric
R834 T828 T829 arg1Of protein,was
R835 T830 T829 arg2Of analyzed,was
R836 T828 T830 arg2Of protein,analyzed
R837 T834 T830 arg3Of and,analyzed
R838 T834 T831 arg1Of and,(
R839 T834 T832 arg1Of and,Fig.
R840 T833 T834 arg1Of 1B,and
R841 T835 T834 arg2Of fig,and
R842 T836 T837 arg1Of S1,)
R843 T840 T838 arg1Of conformation,The
R844 T840 T839 arg1Of conformation,trimeric
R845 T840 T841 arg1Of conformation,of
R846 T844 T841 arg2Of material,of
R847 T844 T842 arg1Of material,the
R848 T844 T843 arg2Of material,purified
R849 T840 T845 arg1Of conformation,was
R850 T846 T845 arg2Of validated,was
R851 T840 T846 arg2Of conformation,validated
R852 T846 T847 arg1Of validated,by
R853 T848 T847 arg2Of using,by
R854 T850 T848 arg2Of EM,using
R855 T850 T849 arg1Of EM,negative-stain
R856 T850 T851 arg1Of EM,(
R857 T853 T851 arg2Of 1C,(
R858 T854 T851 arg3Of ),(
R859 T853 T852 arg1Of 1C,Fig.

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T26 63-70 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 127-134 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 441-448 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T29 493-500 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 998-1005 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T22 63-70 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T23 127-134 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24 441-448 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 465-472 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T26 493-500 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T27 651-662 Chemical denotes Gly-Ser-Ala http://purl.obolibrary.org/obo/CHEBI_163987
T28 663-666 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T30 998-1005 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T20 50-60 Species denotes SARS-CoV-2 NCBItxid:2697049
T21 480-490 Species denotes SARS-CoV-2 NCBItxid:2697049
T22 898-908 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T33 0-418 Sentence denotes To resolve the site-specific glycosylation of the SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo–electron microscopy (cryo-EM) structure, albeit without a glycan-processing blockade using kifunensine (4).
T34 419-511 Sentence denotes This variant of the S protein contains all 22 glycans on the SARS-CoV-2 S protein (Fig. 1A).
T35 512-768 Sentence denotes Stabilization of the trimeric prefusion structure was achieved by using the 2P stabilizing mutations (20) at residues 986 and 987, a GSAS (Gly-Ser-Ala-Ser) substitution at the furin cleavage site (residues 682 to 685), and a C-terminal trimerization motif.
T36 769-841 Sentence denotes This helps to maintain quaternary architecture during glycan processing.
T37 842-1041 Sentence denotes Before analysis, supernatant containing the recombinant SARS-CoV-2 S was purified by size exclusion chromatography to ensure that only native-like trimeric protein was analyzed (Fig. 1B and fig. S1).
T38 1042-1144 Sentence denotes The trimeric conformation of the purified material was validated by using negative-stain EM (Fig. 1C).

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T20 50-60 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T21 480-490 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T22 898-908 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
138 439-448 Gene denotes S protein Gene:43740568
139 491-500 Gene denotes S protein Gene:43740568
140 61-70 Gene denotes S protein Gene:43740568
141 909-910 Gene denotes S Gene:43740568
142 50-60 Species denotes SARS-CoV-2 Tax:2697049
143 480-490 Species denotes SARS-CoV-2 Tax:2697049
144 898-908 Species denotes SARS-CoV-2 Tax:2697049
145 402-413 Chemical denotes kifunensine MESH:C065629
146 465-472 Chemical denotes glycans MESH:D011134
147 651-666 Chemical denotes Gly-Ser-Ala-Ser
148 823-829 Chemical denotes glycan MESH:D011134
149 645-649 CellLine denotes GSAS

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T303 61-70 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T336 439-448 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T369 491-500 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T402 688-693 Protein denotes furin https://www.uniprot.org/uniprot/Q9UCZ5|https://www.uniprot.org/uniprot/Q6LBS3|https://www.uniprot.org/uniprot/Q6GTN6|https://www.uniprot.org/uniprot/Q28193|https://www.uniprot.org/uniprot/Q14336|https://www.uniprot.org/uniprot/P23377|https://www.uniprot.org/uniprot/P23188|https://www.uniprot.org/uniprot/P09958

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T23 29-42 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T21 29-42 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T23 29-42 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T33 0-418 Sentence denotes To resolve the site-specific glycosylation of the SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo–electron microscopy (cryo-EM) structure, albeit without a glycan-processing blockade using kifunensine (4).
T34 419-511 Sentence denotes This variant of the S protein contains all 22 glycans on the SARS-CoV-2 S protein (Fig. 1A).
T35 512-768 Sentence denotes Stabilization of the trimeric prefusion structure was achieved by using the 2P stabilizing mutations (20) at residues 986 and 987, a GSAS (Gly-Ser-Ala-Ser) substitution at the furin cleavage site (residues 682 to 685), and a C-terminal trimerization motif.
T36 769-841 Sentence denotes This helps to maintain quaternary architecture during glycan processing.
T37 842-1041 Sentence denotes Before analysis, supernatant containing the recombinant SARS-CoV-2 S was purified by size exclusion chromatography to ensure that only native-like trimeric protein was analyzed (Fig. 1B and fig. S1).
T38 1042-1144 Sentence denotes The trimeric conformation of the purified material was validated by using negative-stain EM (Fig. 1C).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
138 439-448 Gene denotes S protein Gene:43740568
139 491-500 Gene denotes S protein Gene:43740568
140 61-70 Gene denotes S protein Gene:43740568
141 909-910 Gene denotes S Gene:43740568
142 50-60 Species denotes SARS-CoV-2 Tax:2697049
143 480-490 Species denotes SARS-CoV-2 Tax:2697049
144 898-908 Species denotes SARS-CoV-2 Tax:2697049
145 402-413 Chemical denotes kifunensine MESH:C065629
146 465-472 Chemical denotes glycans MESH:D011134
147 651-666 Chemical denotes Gly-Ser-Ala-Ser
148 823-829 Chemical denotes glycan MESH:D011134
149 645-649 CellLine denotes GSAS