8DM2

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein (focused refinement of NTD)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	Spike glycoprotein	polymer	1285	142441.8	1	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	B	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	1	In PDB GlyTouCan (G42666HT)
3	A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	4	Chemie (NAG)

Sequence modifications

A: 1 - 1208 (UniProt: P0DTC2)

PDB	External Database	Details
Ile 19	Thr 19	conflict
-	Leu 24	deletion
-	Pro 25	deletion
-	Pro 26	deletion
Ser 27	Ala 27	conflict
Asp 142	Gly 142	conflict
Gly 213	Val 213	conflict
Asp 339	Gly 339	conflict
Phe 371	Ser 371	conflict
Pro 373	Ser 373	conflict
Phe 375	Ser 375	conflict
Ala 376	Thr 376	conflict
Asn 405	Asp 405	conflict
Ser 408	Arg 408	conflict
Asn 417	Lys 417	conflict
Lys 440	Asn 440	conflict
Asn 477	Ser 477	conflict
Lys 478	Thr 478	conflict
Ala 484	Glu 484	conflict
Arg 493	Gln 493	conflict
Arg 498	Gln 498	conflict
Tyr 501	Asn 501	conflict
His 505	Tyr 505	conflict
Gly 614	Asp 614	conflict
Tyr 655	His 655	conflict
Lys 679	Asn 679	conflict
His 681	Pro 681	conflict
Gly 682	Arg 682	conflict
Ser 683	Arg 683	conflict
Ser 685	Arg 685	conflict
Lys 764	Asn 764	conflict
Tyr 796	Asp 796	conflict
Pro 817	Phe 817	conflict
Pro 892	Ala 892	conflict
Pro 899	Ala 899	conflict
Pro 942	Ala 942	conflict
His 954	Gln 954	conflict
Lys 969	Asn 969	conflict
Pro 986	Lys 986	conflict
Pro 987	Val 987	conflict
Gly 1209	-	expression tag
Ser 1210	-	expression tag
Gly 1211	-	expression tag
Tyr 1212	-	expression tag
Ile 1213	-	expression tag
Pro 1214	-	expression tag
Glu 1215	-	expression tag
Ala 1216	-	expression tag
Pro 1217	-	expression tag
Arg 1218	-	expression tag
Asp 1219	-	expression tag
Gly 1220	-	expression tag
Gln 1221	-	expression tag
Ala 1222	-	expression tag
Tyr 1223	-	expression tag
Val 1224	-	expression tag
Arg 1225	-	expression tag
Lys 1226	-	expression tag
Asp 1227	-	expression tag
Gly 1228	-	expression tag
Glu 1229	-	expression tag
Trp 1230	-	expression tag
Val 1231	-	expression tag
Leu 1232	-	expression tag
Leu 1233	-	expression tag
Ser 1234	-	expression tag
Thr 1235	-	expression tag
Phe 1236	-	expression tag
Leu 1237	-	expression tag
Gly 1238	-	expression tag
Arg 1239	-	expression tag
Ser 1240	-	expression tag
Leu 1241	-	expression tag
Glu 1242	-	expression tag
Val 1243	-	expression tag
Leu 1244	-	expression tag
Phe 1245	-	expression tag
Gln 1246	-	expression tag
Gly 1247	-	expression tag
Pro 1248	-	expression tag
Gly 1249	-	expression tag
His 1250	-	expression tag
His 1251	-	expression tag
His 1252	-	expression tag
His 1253	-	expression tag
His 1254	-	expression tag
His 1255	-	expression tag
His 1256	-	expression tag
His 1257	-	expression tag
Ser 1258	-	expression tag
Ala 1259	-	expression tag
Trp 1260	-	expression tag
Ser 1261	-	expression tag
His 1262	-	expression tag
Pro 1263	-	expression tag
Gln 1264	-	expression tag
Phe 1265	-	expression tag
Glu 1266	-	expression tag
Lys 1267	-	expression tag
Gly 1268	-	expression tag
Gly 1269	-	expression tag
Gly 1270	-	expression tag
Ser 1271	-	expression tag
Gly 1272	-	expression tag
Gly 1273	-	expression tag
Gly 1274	-	expression tag
Gly 1275	-	expression tag
Ser 1276	-	expression tag
Gly 1277	-	expression tag
Gly 1278	-	expression tag
Ser 1279	-	expression tag
Ala 1280	-	expression tag
Trp 1281	-	expression tag
Ser 1282	-	expression tag
His 1283	-	expression tag
Pro 1284	-	expression tag
Gln 1285	-	expression tag
Phe 1286	-	expression tag
Glu 1287	-	expression tag
Lys 1288	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	1
	Total formula weight	142441.8
Branched	Number of molecules	1
	Total formula weight	424.4
Non-Polymers*	Number of molecules	4
	Total formula weight	884.8
All*	Total formula weight	143751.0

*Water molecules are not included.