9TMF

Structure of the SARS-CoV-2 BA.2.87.1 spike protein ectodomain

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,Fibritin	polymer	1263	139530.5	3	UniProt (P0DTC2) UniProt (P10104) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Severe acute respiratory syndrome coronavirus	S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein
2	D, F, G, I, J... (D, F, G, I, J...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	6	In PDB GlyTouCan (G42666HT)
3	E, H, K (E, H, K)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	3	In PDB GlyTouCan (G15407YE)
4	AA, BA, CA, DA, EA... (B, C, A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	36	Chemie (NAG) PubChem (24139)

Sequence modifications

A, B, C: 26 - 1201 (UniProt: P0DTC2)

PDB	External Database	Details
-	Cys 15	deletion
-	Val 16	deletion
-	Asn 17	deletion
-	Leu 18	deletion
-	Thr 19	deletion
-	Thr 20	deletion
-	Arg 21	deletion
-	Thr 22	deletion
-	Gln 23	deletion
-	Leu 24	deletion
-	Pro 25	deletion
-	Pro 26	deletion
Ser 40	Ala 27	variant
-	His 69	deletion
-	Val 70	deletion
Asp 86	Gly 75	variant
Phe 109	Ser 98	conflict
Ala 137	Val 126	conflict
-	Cys 136	deletion
-	Asn 137	deletion
-	Asp 138	deletion
-	Pro 139	deletion
-	Phe 140	deletion
-	Leu 141	deletion
-	Gly 142	deletion
-	Val 143	deletion
-	Tyr 144	deletion
-	Tyr 145	deletion
-	His 146	deletion
Leu 152	Trp 152	variant
Ser 190	Arg 190	variant
Gly 213	Val 213	variant
Gly 215	Asp 215	variant
Asp 339	Gly 339	variant
Phe 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Ala 376	Thr 376	variant
Asn 405	Asp 405	variant
Ser 408	Arg 408	variant
Thr 417	Lys 417	variant
Lys 440	Asn 440	variant
Asn 444	Lys 444	conflict
Gly 445	Val 445	conflict
Met 452	Leu 452	variant
Lys 460	Asn 460	variant
Asn 477	Ser 477	variant
Lys 481	Asn 481	conflict
Ala 484	Glu 484	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Gly 614	Asp 614	variant
Ser 621	Pro 621	conflict
Gly 642	Val 642	conflict
Tyr 655	His 655	variant
Arg 679	Asn 679	engineered mutation
His 681	Pro 681	engineered mutation
Gly 682	Arg 682	engineered mutation
Ser 683	Arg 683	engineered mutation
Ser 685	Arg 685	engineered mutation
Pro 691	Ser 691	conflict
Lys 764	Asn 764	variant
Ile 791	Thr 791	conflict
His 796	Asp 796	variant
Pro 817	Phe 817	conflict
Pro 892	Ala 892	conflict
Pro 899	Ala 899	conflict
Gly 936	Asp 936	conflict
Pro 942	Ala 942	conflict
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Pro 986	Lys 986	engineered mutation
Pro 987	Val 987	engineered mutation
Glu 1202	-	linker
Leu 1203	-	linker
Gly 1204	-	linker
Lys 1205	-	linker
Tyr 1206	-	linker
Glu 1207	-	linker
Gln 1208	-	linker
Gly 1209	-	linker
Ser 1210	-	linker

A, B, C: 1211 - 1237 (UniProt: P10104)

PDB	External Database	Details
Leu 1232	Phe 479	engineered mutation
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	3
	Total formula weight	418591.6
Branched	Number of molecules	9
	Total formula weight	4306.0
Non-Polymers*	Number of molecules	36
	Total formula weight	7963.5
All*	Total formula weight	430861.2

*Water molecules are not included.