8Y5J

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein

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	Spike glycoprotein	polymer	1248	138697.1	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	3	In PDB GlyTouCan (G42666HT)
3	G	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	1	In PDB GlyTouCan (G15407YE)
4	C, A, B	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	26	Chemie (NAG)

Sequence modifications

A, B, C: 0 - 1207 (UniProt: P0DTC2)

PDB	External Database	Details
Met 16	-	insertion
Pro 17	Asn 17	variant
Phe 19	Thr 19	variant
Asn 20	Thr 20	variant
Leu 21	Arg 21	variant
Ile 22	Thr 22	variant
Thr 23	Gln 23	variant
Thr 24	Leu 24	variant
Thr 25	Pro 25	variant
Gln 26	Pro 26	variant
Ser 27	Ala 27	variant
Leu 50	Ser 50	variant
-	His 69	deletion
-	Val 70	deletion
Phe 127	Val 127	variant
Asp 143	Gly 142	variant
-	Tyr 144	deletion
Ser 157	Phe 157	variant
Gly 158	Arg 158	variant
-	Asn 211	deletion
Ile 212	Leu 212	variant
Gly 213	Val 213	variant
Phe 216	Leu 216	variant
Asn 245	His 245	variant
Asp 264	Ala 264	variant
Val 332	Ile 332	variant
His 339	Gly 339	variant
Thr 356	Lys 356	variant
Phe 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Ala 376	Thr 376	variant
Lys 403	Arg 403	variant
Asn 405	Asp 405	variant
Ser 408	Arg 408	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
His 445	Val 445	variant
Ser 446	Gly 446	variant
Asp 450	Asn 450	variant
Trp 452	Leu 452	variant
Ser 455	Leu 455	variant
Lys 460	Asn 460	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Lys 481	Asn 481	variant
-	Val 483	deletion
Lys 483	Glu 484	variant
Pro 485	Phe 486	variant
Arg 497	Gln 498	variant
Tyr 500	Asn 501	variant
His 504	Tyr 505	variant
Lys 553	Glu 554	variant
Val 569	Ala 570	variant
Gly 613	Asp 614	variant
Ser 620	Pro 621	variant
Tyr 654	His 655	variant
Val 669	Ile 670	variant
Lys 678	Asn 679	variant
Arg 680	Pro 681	variant
Lys 763	Asn 764	variant
Tyr 795	Asp 796	variant
Pro 816	Phe 817	engineered mutation
Pro 891	Ala 892	engineered mutation
Pro 898	Ala 899	engineered mutation
Phe 938	Ser 939	variant
Pro 941	Ala 942	engineered mutation
His 953	Gln 954	variant
Lys 968	Asn 969	variant
Pro 985	Lys 986	engineered mutation
Pro 986	Val 987	engineered mutation
Leu 1142	Pro 1143	variant
Gly 1208	-	expression tag
Gly 1209	-	expression tag
Gly 1210	-	expression tag
Ser 1211	-	expression tag
Gly 1212	-	expression tag
Tyr 1213	-	expression tag
Ile 1214	-	expression tag
Pro 1215	-	expression tag
Glu 1216	-	expression tag
Ala 1217	-	expression tag
Pro 1218	-	expression tag
Arg 1219	-	expression tag
Asp 1220	-	expression tag
Gly 1221	-	expression tag
Gln 1222	-	expression tag
Ala 1223	-	expression tag
Tyr 1224	-	expression tag
Val 1225	-	expression tag
Arg 1226	-	expression tag
Lys 1227	-	expression tag
Asp 1228	-	expression tag
Gly 1229	-	expression tag
Glu 1230	-	expression tag
Trp 1231	-	expression tag
Val 1232	-	expression tag
Leu 1233	-	expression tag
Leu 1234	-	expression tag
Ser 1235	-	expression tag
Thr 1236	-	expression tag
Phe 1237	-	expression tag
Leu 1238	-	expression tag
Gly 1239	-	expression tag
Gly 1240	-	expression tag
Gly 1241	-	expression tag
Ser 1242	-	expression tag
Ala 1243	-	expression tag
Trp 1244	-	expression tag
Ser 1245	-	expression tag
His 1246	-	expression tag
Pro 1247	-	expression tag
Gln 1248	-	expression tag
Phe 1249	-	expression tag
Glu 1250	-	expression tag
Lys 1251	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	416091.4
Branched	Number of molecules	4
	Total formula weight	1859.7
Non-Polymers*	Number of molecules	26
	Total formula weight	5751.4
All*	Total formula weight	423702.5

*Water molecules are not included.