7XOE

Cryo-EM structure of S glycoprotein encoded by the Covid-19 mRNA vaccine candidate RQ3013 (Prefusion state)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0016020	cellular_component	membrane
A	0019031	cellular_component	viral envelope
A	0019064	biological_process	fusion of virus membrane with host plasma membrane
A	0039654	biological_process	fusion of virus membrane with host endosome membrane
A	0046813	biological_process	receptor-mediated virion attachment to host cell
A	0055036	cellular_component	virion membrane
A	0075509	biological_process	endocytosis involved in viral entry into host cell
B	0016020	cellular_component	membrane
B	0019031	cellular_component	viral envelope
B	0019064	biological_process	fusion of virus membrane with host plasma membrane
B	0039654	biological_process	fusion of virus membrane with host endosome membrane
B	0046813	biological_process	receptor-mediated virion attachment to host cell
B	0055036	cellular_component	virion membrane
B	0075509	biological_process	endocytosis involved in viral entry into host cell
C	0016020	cellular_component	membrane
C	0019031	cellular_component	viral envelope
C	0019064	biological_process	fusion of virus membrane with host plasma membrane
C	0039654	biological_process	fusion of virus membrane with host endosome membrane
C	0046813	biological_process	receptor-mediated virion attachment to host cell
C	0055036	cellular_component	virion membrane
C	0075509	biological_process	endocytosis involved in viral entry into host cell

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3597
Details	TOPO_DOM: Extracellular => ECO:0000255|HAMAP-Rule:MF_04099

Chain	Residue	Details
A	GLN14-ILE1213
B	GLN14-ILE1213
C	GLN14-ILE1213

---

site_id	SWS_FT_FI2
Number of Residues	60
Details	TRANSMEM: Helical => ECO:0000255|HAMAP-Rule:MF_04099

Chain	Residue	Details
A	TRP1214-MET1234
B	TRP1214-MET1234
C	TRP1214-MET1234

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	SITE: Cleavage; by host furin => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32142651, ECO:0000269|PubMed:32362314, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616

Chain	Residue	Details
A	ALA685
B	ALA685
C	ALA685

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	SITE: Cleavage; by host TMPRSS2 or CTSL => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616

Chain	Residue	Details
A	ILE815
B	ILE815
C	ILE815

---

site_id	SWS_FT_FI5
Number of Residues	15
Details	LIPID: S-palmitoyl cysteine; by host ZDHHC20 => ECO:0000269|PubMed:34599882

Chain	Residue	Details
A	THR1235
B	GLY1243
C	THR1235
C	SER1236
C	CYS1240
C	LEU1241
C	GLY1243
A	SER1236
A	CYS1240
A	LEU1241
A	GLY1243
B	THR1235
B	SER1236
B	CYS1240
B	LEU1241

---

site_id	SWS_FT_FI6
Number of Residues	15
Details	LIPID: S-palmitoyl cysteine; by host ZDHHC20; partial => ECO:0000269|PubMed:34599882

Chain	Residue	Details
A	CYS1247
B	SER1254
C	CYS1247
C	GLY1248
C	CYS1250
C	GLY1253
C	SER1254
A	GLY1248
A	CYS1250
A	GLY1253
A	SER1254
B	CYS1247
B	GLY1248
B	CYS1250
B	GLY1253

---

site_id	SWS_FT_FI7
Number of Residues	9
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	ASN17
A	SER1158
A	VAL1173
B	ASN17
B	SER1158
B	VAL1173
C	ASN17
C	SER1158
C	VAL1173

---

site_id	SWS_FT_FI8
Number of Residues	15
Details	CARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	ASN61
B	THR1074
C	ASN61
C	THR122
C	ILE717
C	GLN801
C	THR1074
A	THR122
A	ILE717
A	GLN801
A	THR1074
B	ASN61
B	THR122
B	ILE717
B	GLN801

---

site_id	SWS_FT_FI9
Number of Residues	9
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	THR74
A	TRP149
A	LEU1194
B	THR74
B	TRP149
B	LEU1194
C	THR74
C	TRP149
C	LEU1194

---

site_id	SWS_FT_FI10
Number of Residues	21
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	PHE165
B	ASN331
B	ARG343
B	GLU616
B	TYR657
B	HIS1098
C	PHE165
C	ILE282
C	ASN331
C	ARG343
C	GLU616
A	ILE282
C	TYR657
C	HIS1098
A	ASN331
A	ARG343
A	GLU616
A	TYR657
A	HIS1098
B	PHE165
B	ILE282

---

site_id	SWS_FT_FI11
Number of Residues	6
Details	CARBOHYD: N-linked (GlcNAc...) (high mannose) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	ARG234
A	ILE709
B	ARG234
B	ILE709
C	ARG234
C	ILE709

---

site_id	SWS_FT_FI12
Number of Residues	3
Details	CARBOHYD: O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391

Chain	Residue	Details
A	ILE323
B	ILE323
C	ILE323

---

site_id	SWS_FT_FI13
Number of Residues	3
Details	CARBOHYD: O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391

Chain	Residue	Details
A	ARG325
B	ARG325
C	ARG325

---

site_id	SWS_FT_FI14
Number of Residues	3
Details	CARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	ASN603
B	ASN603
C	ASN603

---

site_id	SWS_FT_FI15
Number of Residues	6
Details	CARBOHYD: O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583

Chain	Residue	Details
A	ASN676
A	HIS678
B	ASN676
B	HIS678
C	ASN676
C	HIS678

---

site_id	SWS_FT_FI16
Number of Residues	3
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942

Chain	Residue	Details
A	VAL1134
B	VAL1134
C	VAL1134

---