IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. bioRxiv : the preprint server for biology 2020 imex curation Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 3d-em 3D electron microscopy 3D-EM electron tomog structure determination identification by structure determination identification by structure determination structure determination Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov Accepted 2020-SEP-15 AT 10:11 BST AT 10:11 BST by KALPANAP bioRxiv : the preprint server for biology 2020 Only protein-protein interactions imex curation imex curation A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. bioRxiv : the preprint server for biology 2020 imex curation Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined pH 4.5 7.4 5.5 Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov Accepted 2020-SEP-15 AT 10:11 BST AT 10:11 BST by KALPANAP bioRxiv : the preprint server for biology 2020 Only protein-protein interactions imex curation imex curation A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. bioRxiv : the preprint server for biology 2020 imex curation Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro bio-layer interferometry bio-layer interferometry bli bli predetermined predetermined participant predetermined pH 7.4 4.0 Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov Accepted 2020-SEP-15 AT 10:11 BST AT 10:11 BST by KALPANAP bioRxiv : the preprint server for biology 2020 Only protein-protein interactions imex curation imex curation A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. bioRxiv : the preprint server for biology 2020 imex curation Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Zhou T., Zhou T., Tsybovsky Y., Olia AS., Gorman J., Rapp MA., Cerutti G., Katsamba PS., Nazzari A., Schon A., Wang PD., Bimela J., Shi W., Teng IT., Zhang B., Boyington JC., Chuang GY., Sampson JM., Sastry M., Stephens T., Stuckey J., Wang S., Friesner RA., Ho DD., Mascola JR., Shapiro L., Kwong PD. Virus - Publications including interactions involving viral proteins It has been assumed that the Spike protein trimerisation tag is still present, as the FQ/GP HRV3C cleavage site is AFTER this tag, thus the rest of the tags will have been removed. However the PDBe entries still give all tags as being retained. was unassigned 253. Authors did not reply to email. lss8@columbia.edu,pdkwong@nih.gov Accepted 2020-SEP-15 AT 10:11 BST AT 10:11 BST by KALPANAP bioRxiv : the preprint server for biology 2020 Only protein-protein interactions imex curation imex curation ace2_human Angiotensin-converting enzyme 2 ACE2 UNQ868/PRO1885 Angiotensin-converting enzyme homolog Metalloprotease MPROT15 Angiotensin-converting enzyme-related carboxypeptidase protein protein human Homo sapiens Human MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENNPGFQNTDDVQTSF mint Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin-13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. In case of human coronaviruses SARS and HCoV-NL63 infections, serve as functional receptor for the spike glycoprotein of both coronaviruses 8EE6EB0A931550E8 spike_sars2 Spike glycoprotein S E2 Peplomer protein 2 protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT ace2-s-54 9 10 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 11 unspecified role unspecified role neutral component neutral component purified purified T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain R S certain certain sequence position certain certain certain sequence position certain RR GS human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction 1B It is stated that 1.9 ACE2 molecules bound per spike trimer. Spike is capable of recognizing ACE2 even in the presence of antibody (Fab) CR3022. s-37 1 11 unspecified role unspecified role neutral component neutral component purified purified region carbohydrate chemical modification carbohydrate chemical modification carbohydrate chemical modification undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP Tue Jun 30 17:36:26 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Lys986_Val987delinsProPro' P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain RR GS certain certain sequence position certain certain certain sequence position certain R S Tue Jun 30 19:20:40 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Arg682_Arg683delinsGlySer;Arg685Ser]' physical association physical association Extended Data 5 +6 ace2-s-51 6 10 unspecified role unspecified role bait bait purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain C-terminus fc-igg tag fc-igg tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 11 unspecified role unspecified role prey prey purified purified T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain R S certain certain sequence position certain certain certain sequence position certain RR GS P0DTC2:p.Asp614Gly mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain D G human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction 7 5E ace2-s-55 6 10 unspecified role unspecified role bait bait purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain C-terminus fc-igg tag fc-igg tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 11 unspecified role unspecified role prey prey purified purified T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain R S certain certain sequence position certain certain certain sequence position certain RR GS P0DTC2:p.Asp614Gly mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain D G human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction 8 5E ace2-s-57 2 10 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 11 unspecified role unspecified role bait bait purified purified region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain R S certain certain sequence position certain certain certain sequence position certain RR GS rbd sufficient to bind sufficient binding region sufficient to bind range range range range human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction 7 Supp. Figure 3B It is stated:-"fit to a 1:1 interaction model" - how this can be reconciled with a 2:3 ratio from earlier I do not know - so left blank. (the Spike is a trimer.) s-ace2-38 2 10 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 11 unspecified role unspecified role bait bait purified purified region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain R S certain certain sequence position certain certain certain sequence position certain RR GS rbd sufficient to bind sufficient binding region sufficient to bind range range range range human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction 5 Supp. Figure 3B It is stated:-"fit to a 1:1 interaction model" - how this can be reconciled with a 2:3 ratio from earlier I do not know - so left blank. (the Spike is a trimer.) s-ace2-39 2 10 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f 11 unspecified role unspecified role bait bait purified purified region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined T4 phage fibritin trimerization motif tag tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P0DTC2:p.Lys986_Val987delinsProPro mutation mutation certain certain sequence position certain certain certain sequence position certain KV PP P0DTC2:p.[Arg682_Arg683delinsGlySer;Arg685Ser] mutation mutation certain certain sequence position certain certain certain sequence position certain R S certain certain sequence position certain certain certain sequence position certain RR GS rbd sufficient to bind sufficient binding region sufficient to bind range range range range human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction 3 Supp. Figure 3B It is stated:-"fit to a 1:1 interaction model" - how this can be reconciled with a 2:3 ratio from earlier I do not know - so left blank. (the Spike is a trimer.)