8Y16

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein in complex with human ACE2

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, E, F (A, E, F)	Angiotensin-converting enzyme 2	polymer	603	69982.6	3	UniProt (Q9BYF1) Pfam (PF01401)	Homo sapiens (human)	ACE-related carboxypeptidase,Angiotensin-converting enzyme homolog,ACEH,Metalloprotease MPROT15
2	B, C, D (B, C, D)	Spike glycoprotein	polymer	1248	138697.1	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
3	G, H, R, S, V... (G, H, R, S, V...)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	6	In PDB GlyTouCan (G15407YE)
4	I, J, K, L, M... (I, J, K, L, M...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	13	In PDB GlyTouCan (G42666HT)
5	HB, KB, Z (E, F, A)	ZINC ION	non-polymer		65.4	3	Chemie (ZN)
6	AA, AB, BA, BB, CA... (A, D, B, E, C...)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	37	Chemie (NAG)

Sequence modifications

A, E, F: 19 - 615 (UniProt: Q9BYF1)

PDB	External Database	Details
His 616	-	expression tag
His 617	-	expression tag
His 618	-	expression tag
His 619	-	expression tag
His 620	-	expression tag
His 621	-	expression tag

B, C, D: 0 - 1208 (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 484	Glu 484	variant
Pro 486	Phe 486	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Lys 554	Glu 554	variant
Val 570	Ala 570	variant
Gly 614	Asp 614	variant
Ser 621	Pro 621	variant
Tyr 655	His 655	variant
Val 670	Ile 670	variant
Lys 679	Asn 679	variant
Arg 681	Pro 681	variant
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
Phe 939	Ser 939	variant
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
Leu 1143	Pro 1143	variant
Gly 1209	-	expression tag
Gly 1210	-	expression tag
Gly 1211	-	expression tag
Ser 1212	-	expression tag
Gly 1213	-	expression tag
Tyr 1214	-	expression tag
Ile 1215	-	expression tag
Pro 1216	-	expression tag
Glu 1217	-	expression tag
Ala 1218	-	expression tag
Pro 1219	-	expression tag
Arg 1220	-	expression tag
Asp 1221	-	expression tag
Gly 1222	-	expression tag
Gln 1223	-	expression tag
Ala 1224	-	expression tag
Tyr 1225	-	expression tag
Val 1226	-	expression tag
Arg 1227	-	expression tag
Lys 1228	-	expression tag
Asp 1229	-	expression tag
Gly 1230	-	expression tag
Glu 1231	-	expression tag
Trp 1232	-	expression tag
Val 1233	-	expression tag
Leu 1234	-	expression tag
Leu 1235	-	expression tag
Ser 1236	-	expression tag
Thr 1237	-	expression tag
Phe 1238	-	expression tag
Leu 1239	-	expression tag
Gly 1240	-	expression tag
Gly 1241	-	expression tag
Gly 1242	-	expression tag
Ser 1243	-	expression tag
Ala 1244	-	expression tag
Trp 1245	-	expression tag
Ser 1246	-	expression tag
His 1247	-	expression tag
Pro 1248	-	expression tag
Gln 1249	-	expression tag
Phe 1250	-	expression tag
Glu 1251	-	expression tag
Lys 1252	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	6
	Total formula weight	626039.1
Branched	Number of molecules	19
	Total formula weight	9036.5
Non-Polymers*	Number of molecules	40
	Total formula weight	8380.9
All*	Total formula weight	643456.4

*Water molecules are not included.