8XLV

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P), 1-RBD-up state

This is a non-PDB format compatible entry.

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	Spike glycoprotein	polymer	1191	131772.4	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, E, F, G, H...	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	B, C, A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	24	Chemie (NAG)

Sequence modifications

A, B, C: 28 - 1146 (UniProt: P0DTC2)

PDB	External Database	Details
Met 0	-	initiating methionine
Phe 1	-	expression tag
Val 2	-	expression tag
Phe 3	-	expression tag
Leu 4	-	expression tag
Val 5	-	expression tag
Leu 6	-	expression tag
Leu 7	-	expression tag
Pro 8	-	expression tag
Leu 9	-	expression tag
Val 10	-	expression tag
Ser 11	-	expression tag
Ser 12	-	expression tag
Gln 13	-	expression tag
Cys 14	-	expression tag
Val 15	-	expression tag
Met 16	-	expression tag
Pro 17	-	expression tag
Leu 18	-	expression tag
Phe 19	-	expression tag
Asn 20	-	expression tag
Leu 21	-	expression tag
Ile 22	-	expression tag
Thr 23	-	expression tag
Thr 24	-	expression tag
Thr 25	-	expression tag
Gln 26	-	expression tag
Ser 27	-	expression tag
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
Lys 460	Asn 460	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Lys 481	Asn 481	variant
-	Val 483	deletion
Lys 483	Glu 484	variant
Pro 485	Phe 486	variant
Arg 497	Gln 498	variant
Tyr 500	Asn 501	variant
His 504	Tyr 505	variant
Lys 553	Glu 554	variant
Val 569	Ala 570	variant
Gly 613	Asp 614	variant
Ser 620	Pro 621	variant
Tyr 654	His 655	variant
Val 669	Ile 670	variant
Lys 678	Asn 679	variant
Arg 680	Pro 681	variant
Gly 681	Arg 682	engineered mutation
Ser 682	Arg 683	engineered mutation
Ser 684	Arg 685	engineered mutation
Lys 763	Asn 764	variant
Tyr 795	Asp 796	variant
Pro 816	Phe 817	engineered mutation
Pro 891	Ala 892	engineered mutation
Pro 898	Ala 899	engineered mutation
Phe 938	Ser 939	variant
Pro 941	Ala 942	engineered mutation
His 953	Gln 954	variant
Lys 968	Asn 969	variant
Pro 985	Lys 986	engineered mutation
Pro 986	Val 987	engineered mutation
Leu 1142	Pro 1143	variant
Gly 1147	-	expression tag
Gly 1148	-	expression tag
Gly 1149	-	expression tag
Ser 1150	-	expression tag
Gly 1151	-	expression tag
Gly 1152	-	expression tag
Gly 1153	-	expression tag
Ser 1154	-	expression tag
Gly 1155	-	expression tag
Tyr 1156	-	expression tag
Ile 1157	-	expression tag
Pro 1158	-	expression tag
Glu 1159	-	expression tag
Ala 1160	-	expression tag
Pro 1161	-	expression tag
Arg 1162	-	expression tag
Asp 1163	-	expression tag
Gly 1164	-	expression tag
Gln 1165	-	expression tag
Ala 1166	-	expression tag
Tyr 1167	-	expression tag
Val 1168	-	expression tag
Arg 1169	-	expression tag
Lys 1170	-	expression tag
Asp 1171	-	expression tag
Gly 1172	-	expression tag
Glu 1173	-	expression tag
Trp 1174	-	expression tag
Val 1175	-	expression tag
Leu 1176	-	expression tag
Leu 1177	-	expression tag
Ser 1178	-	expression tag
Thr 1179	-	expression tag
Phe 1180	-	expression tag
Leu 1181	-	expression tag
Gly 1182	-	expression tag
Gly 1183	-	expression tag
Gly 1184	-	expression tag
Ser 1185	-	expression tag
Ala 1186	-	expression tag
Trp 1187	-	expression tag
Ser 1188	-	expression tag
His 1189	-	expression tag
Pro 1190	-	expression tag
Gln 1191	-	expression tag
Phe 1192	-	expression tag
Glu 1193	-	expression tag
Lys 1194	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	395317.2
Branched	Number of molecules	6
	Total formula weight	2546.4
Non-Polymers*	Number of molecules	24
	Total formula weight	5309.0
All*	Total formula weight	403172.6

*Water molecules are not included.