8JYO

Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, C (A, B, C)	Spike glycoprotein	polymer	1245	138086.1	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2)	S glycoprotein,E2,Peplomer protein
2	D, E (E, D)	Processed angiotensin-converting enzyme 2	polymer	608	70485.1	2	UniProt (Q9BYF1) Pfam (PF01401)	Homo sapiens (human)
3	F, G, H, I, J... (F, G, H, I, J...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	9	In PDB GlyTouCan (G42666HT)
4	N, Q (N, Q)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	2	In PDB GlyTouCan (G15407YE)
5	O, R (O, R)	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		910.8	2	In PDB GlyTouCan (G22768VO)
6	AA, AB, BA, BB, CA... (A, C, E, B, D)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	42	Chemie (NAG)

Sequence modifications

A, B, C: 28 - 1210 (UniProt: P0DTC2)

PDB	External Database	Details
Leu 5	-	expression tag
Leu 6	-	expression tag
Met 7	-	expression tag
Gly 8	-	expression tag
Cys 9	-	expression tag
Val 10	-	expression tag
Ala 11	-	expression tag
Glu 12	-	expression tag
Thr 13	-	expression tag
Gly 14	-	expression tag
Ser 15	-	expression tag
Ser 16	-	expression tag
Gln 17	-	expression tag
Cys 18	-	expression tag
Val 19	-	expression tag
Asn 20	-	expression tag
Leu 21	-	expression tag
Ile 22	-	expression tag
Thr 23	-	expression tag
Arg 24	-	expression tag
Thr 25	-	expression tag
Gln 26	-	expression tag
Ser 27	-	expression tag
Ala 83	Val 83	variant
Asp 142	Gly 142	variant
-	Tyr 144	deletion
Gln 146	His 146	variant
Glu 183	Gln 183	variant
Glu 213	Val 213	variant
Val 252	Gly 252	variant
His 339	Gly 339	variant
Thr 346	Arg 346	variant
Ile 368	Leu 368	variant
Phe 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Ala 376	Thr 376	variant
Asn 405	Asp 405	variant
Ser 408	Arg 408	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
Pro 445	Val 445	variant
Ser 446	Gly 446	variant
Lys 460	Asn 460	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Pro 486	Phe 486	variant
Ser 490	Phe 490	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Gly 614	Asp 614	variant
Tyr 655	His 655	variant
Lys 679	Asn 679	variant
His 681	Pro 681	variant
Gly 682	Arg 682	engineered mutation
Ser 683	Arg 683	engineered mutation
Gly 685	Arg 685	engineered mutation
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Pro 817	Phe 817	engineered mutation
Pro 892	Ala 892	engineered mutation
Pro 899	Ala 899	engineered mutation
Pro 942	Ala 942	engineered mutation
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Pro 986	Lys 986	engineered mutation
Pro 987	Val 987	engineered mutation
Ala 1211	-	expression tag
Ser 1212	-	expression tag
Ser 1213	-	expression tag
Gly 1214	-	expression tag
Tyr 1215	-	expression tag
Ile 1216	-	expression tag
Pro 1217	-	expression tag
Glu 1218	-	expression tag
Ala 1219	-	expression tag
Pro 1220	-	expression tag
Arg 1221	-	expression tag
Asp 1222	-	expression tag
Gly 1223	-	expression tag
Gln 1224	-	expression tag
Ala 1225	-	expression tag
Tyr 1226	-	expression tag
Val 1227	-	expression tag
Arg 1228	-	expression tag
Lys 1229	-	expression tag
Asp 1230	-	expression tag
Gly 1231	-	expression tag
Glu 1232	-	expression tag
Trp 1233	-	expression tag
Val 1234	-	expression tag
Leu 1235	-	expression tag
Leu 1236	-	expression tag
Ser 1237	-	expression tag
Thr 1238	-	expression tag
Phe 1239	-	expression tag
Leu 1240	-	expression tag
Glu 1241	-	expression tag
Gly 1242	-	expression tag
Thr 1243	-	expression tag
Lys 1244	-	expression tag
His 1245	-	expression tag
His 1246	-	expression tag
His 1247	-	expression tag
His 1248	-	expression tag
His 1249	-	expression tag
His 1250	-	expression tag

E, D: 19 - 617 (UniProt: Q9BYF1)

PDB	External Database	Details
Gly 618	-	expression tag
Thr 619	-	expression tag
Lys 620	-	expression tag
His 621	-	expression tag
His 622	-	expression tag
His 623	-	expression tag
His 624	-	expression tag
His 625	-	expression tag
His 626	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	5
	Total formula weight	555228.5
Branched	Number of molecules	13
	Total formula weight	6814.3
Non-Polymers*	Number of molecules	42
	Total formula weight	9290.7
All*	Total formula weight	571333.6

*Water molecules are not included.