7UZ8

Structure of the SARS-CoV-2 Omicron BA.1 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31

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	1253	139503.2	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, H (H, M, P)	M8a-31 Fab heavy chain	polymer	228	24474.3	3		Mus musculus
3	E, G, I (L, N, Q)	M8a-31 Fab light chain	polymer	220	24188.9	3		Mus musculus
4	J, K, L (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)
5	AA, BA, CA, DA, EA... (B, C, A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	27	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1212 (UniProt: P0DTC2)

PDB	External Database	Details
Val 67	Ala 67	variant
-	His 69	deletion
-	Val 70	deletion
Ile 95	Thr 95	variant
-	Gly 142	deletion
-	Val 143	deletion
-	Tyr 144	deletion
Asp 142	Tyr 145	variant
Ile 212	-	insertion
Val 213	-	insertion
Arg 214	Asn 211	variant
Glu 214	Leu 212	variant
Pro 214	Val 213	variant
Glu 214	Arg 214	variant
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 682	Asn 679	variant
-	Pro 681	deletion
-	Arg 682	deletion
-	Arg 683	deletion
His 684	Ala 684	variant
Ala 685	Arg 685	variant
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
Pro 1213	-	expression tag
Ser 1214	-	expression tag
Gly 1215	-	expression tag
Arg 1216	-	expression tag
Leu 1217	-	expression tag
Val 1218	-	expression tag
Pro 1219	-	expression tag
Arg 1220	-	expression tag
Gly 1221	-	expression tag
Ser 1222	-	expression tag
Pro 1223	-	expression tag
Gly 1224	-	expression tag
Ser 1225	-	expression tag
Gly 1226	-	expression tag
Tyr 1227	-	expression tag
Ile 1228	-	expression tag
Pro 1229	-	expression tag
Glu 1230	-	expression tag
Ala 1231	-	expression tag
Pro 1232	-	expression tag
Arg 1233	-	expression tag
Asp 1234	-	expression tag
Gly 1235	-	expression tag
Gln 1236	-	expression tag
Ala 1237	-	expression tag
Tyr 1238	-	expression tag
Val 1239	-	expression tag
Arg 1240	-	expression tag
Lys 1241	-	expression tag
Asp 1242	-	expression tag
Gly 1243	-	expression tag
Glu 1244	-	expression tag
Trp 1245	-	expression tag
Val 1246	-	expression tag
Leu 1247	-	expression tag
Leu 1248	-	expression tag
Ser 1249	-	expression tag
Thr 1250	-	expression tag
Phe 1251	-	expression tag
Leu 1252	-	expression tag
Gly 1253	-	expression tag
His 1254	-	expression tag
His 1255	-	expression tag
His 1256	-	expression tag
His 1257	-	expression tag
His 1258	-	expression tag
His 1259	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	564499.1
Branched	Number of molecules	3
	Total formula weight	1273.2
Non-Polymers*	Number of molecules	27
	Total formula weight	5972.6
All*	Total formula weight	571744.9

*Water molecules are not included.