8HCA

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (1 RBD up)

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	1240	138036.2	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, F, G (E, L, G)	Light chain of YB13-292 Fab	polymer	219	23976.6	3		Homo sapiens
3	E, H, I (F, H, D)	Heavy chain of YB13-292 Fab	polymer	238	25283.4	3		Homo sapiens
4	J, K, L, M, N... (I, J, K, M, N...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	12	In PDB GlyTouCan (G42666HT)
5	AA, BA, CA, DA, EA... (A, B, C)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	30	Chemie (NAG)

Sequence modifications

A, B, C: 14 - 1211 (UniProt: P0DTC2)

PDB	External Database	Details
Val 67	Ala 67	variant
-	His 69	deletion
-	Val 70	deletion
Ile 95	Thr 95	variant
Asp 142	Gly 142	variant
-	Val 143	deletion
-	Tyr 144	deletion
-	Tyr 145	deletion
-	Asn 211	deletion
Ile 210	Leu 212	variant
Glu 210	-	insertion
Pro 210	-	insertion
Glu 210	-	insertion
Asp 339	Gly 339	variant
Leu 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
Ser 446	Gly 446	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Arg 493	Gln 493	variant
Ser 496	Gly 496	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Lys 547	Thr 547	variant
Gly 614	Asp 614	variant
Tyr 655	His 655	variant
Lys 683	Asn 679	variant
-	Pro 681	deletion
-	Arg 682	deletion
-	Arg 683	deletion
-	Ala 684	deletion
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Pro 817	Phe 817	engineered mutation
Lys 856	Asn 856	variant
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
Phe 981	Leu 981	variant
Pro 986	Lys 986	engineered mutation
Pro 987	Val 987	engineered mutation
Gly 1212	-	expression tag
Ser 1213	-	expression tag
Gly 1214	-	expression tag
Arg 1215	-	expression tag
Glu 1216	-	expression tag
Asn 1217	-	expression tag
Leu 1218	-	expression tag
Tyr 1219	-	expression tag
Phe 1220	-	expression tag
Gln 1221	-	expression tag
Gly 1222	-	expression tag
Gly 1223	-	expression tag
Gly 1224	-	expression tag
Gly 1225	-	expression tag
Ser 1226	-	expression tag
Gly 1227	-	expression tag
Tyr 1228	-	expression tag
Ile 1229	-	expression tag
Pro 1230	-	expression tag
Glu 1231	-	expression tag
Ala 1232	-	expression tag
Pro 1233	-	expression tag
Arg 1234	-	expression tag
Asp 1235	-	expression tag
Gly 1236	-	expression tag
Gln 1237	-	expression tag
Ala 1238	-	expression tag
Tyr 1239	-	expression tag
Val 1240	-	expression tag
Arg 1241	-	expression tag
Lys 1242	-	expression tag
Asp 1243	-	expression tag
Gly 1244	-	expression tag
Glu 1245	-	expression tag
Trp 1246	-	expression tag
Val 1247	-	expression tag
Leu 1248	-	expression tag
Leu 1249	-	expression tag
Ser 1250	-	expression tag
Thr 1251	-	expression tag
Phe 1252	-	expression tag
Leu 1253	-	expression tag
Gly 1254	-	expression tag
His 1255	-	expression tag
His 1256	-	expression tag
His 1257	-	expression tag
His 1258	-	expression tag
His 1259	-	expression tag
His 1260	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	561888.7
Branched	Number of molecules	12
	Total formula weight	5092.8
Non-Polymers*	Number of molecules	30
	Total formula weight	6636.2
All*	Total formula weight	573617.7

*Water molecules are not included.