7Y9S

Cryo-EM structure of apo SARS-CoV-2 Omicron spike protein (S-2P-GSAS)

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	1249	138842.4	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2)	S glycoprotein,E2,Peplomer protein
2	D, E, F, G, H... (D, E, F, G, H...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	16	In PDB GlyTouCan (G42666HT)
3	AA, BA, CA, DA, EA... (A, B, C)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	21	Chemie (NAG)

Sequence modifications

A, B, C: 15 - 1208 (UniProt: P0DTC2)

PDB	External Database	Details
Met -4	-	initiating methionine
Pro -3	-	expression tag
Arg -2	-	expression tag
Gly -1	-	expression tag
Pro 0	-	expression tag
Val 1	-	expression tag
Ala 2	-	expression tag
Ala 3	-	expression tag
Leu 4	-	expression tag
Leu 5	-	expression tag
Leu 6	-	expression tag
Leu 7	-	expression tag
Ile 8	-	expression tag
Leu 9	-	expression tag
His 10	-	expression tag
Gly 11	-	expression tag
Ala 12	-	expression tag
Trp 13	-	expression tag
Ser 14	-	expression tag
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 211	Leu 212	variant
Glu 214	-	insertion
Pro 214	-	insertion
Glu 214	-	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 679	Asn 679	variant
His 681	Pro 681	variant
Gly 682	Arg 682	variant
Ser 683	Arg 683	variant
Ser 685	Arg 685	variant
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Lys 856	Asn 856	variant
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
Leu 1209	-	expression tag
Val 1210	-	expression tag
Pro 1211	-	expression tag
Arg 1212	-	expression tag
Gly 1213	-	expression tag
Ser 1214	-	expression tag
Gly 1215	-	expression tag
Tyr 1216	-	expression tag
Ile 1217	-	expression tag
Pro 1218	-	expression tag
Glu 1219	-	expression tag
Ala 1220	-	expression tag
Pro 1221	-	expression tag
Arg 1222	-	expression tag
Asp 1223	-	expression tag
Gly 1224	-	expression tag
Gln 1225	-	expression tag
Ala 1226	-	expression tag
Tyr 1227	-	expression tag
Val 1228	-	expression tag
Arg 1229	-	expression tag
Lys 1230	-	expression tag
Asp 1231	-	expression tag
Gly 1232	-	expression tag
Glu 1233	-	expression tag
Trp 1234	-	expression tag
Val 1235	-	expression tag
Leu 1236	-	expression tag
Leu 1237	-	expression tag
Ser 1238	-	expression tag
Thr 1239	-	expression tag
Phe 1240	-	expression tag
Leu 1241	-	expression tag
His 1242	-	expression tag
His 1243	-	expression tag
His 1244	-	expression tag
His 1245	-	expression tag
His 1246	-	expression tag
His 1247	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	416527.1
Branched	Number of molecules	16
	Total formula weight	6790.4
Non-Polymers*	Number of molecules	21
	Total formula weight	4645.4
All*	Total formula weight	427962.9

*Water molecules are not included.