8GTP

cryo-EM structure of Omicron BA.5 S protein in complex with XGv289

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	1271	141326.8	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, F, H (H, I, J)	heavy chain of XGv289	polymer	120	13098.6	3		Homo sapiens
3	E, G, I (L, M, N)	light chain of XGv289	polymer	111	11586.7	3		Homo sapiens
4	AA, J, K, L, M... (a, D, E, F, G...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	18	In PDB GlyTouCan (G42666HT)
5	AB, BA, BB, CA, CB... (C, A, B)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	33	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1273 (UniProt: P0DTC2)

PDB	External Database	Details
Ile 19	Thr 19	variant
-	His 69	deletion
-	Val 70	deletion
Asp 142	Gly 142	variant
Gly 213	Val 213	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
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
Arg 452	Leu 452	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Val 486	Phe 486	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Gly 614	Asp 614	variant
Tyr 655	His 655	variant
Lys 679	Asn 679	variant
His 681	Pro 681	variant
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Pro 817	Phe 817	variant
Pro 892	Ala 892	variant
Pro 899	Ala 899	variant
Pro 942	Ala 942	variant
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Pro 986	Lys 986	variant
Pro 987	Val 987	variant

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	498036.2
Branched	Number of molecules	18
	Total formula weight	7639.2
Non-Polymers*	Number of molecules	33
	Total formula weight	7299.9
All*	Total formula weight	512975.3

*Water molecules are not included.