7YAD

Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local refinement)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, D (A, C)	S309 neutralizing antibody heavy chain	polymer	126	13918.4	2		Homo sapiens
2	B, E (B, D)	S309 neutralizing antibody light chain	polymer	108	11601.9	2		Homo sapiens
3	C, F (M, E)	Spike protein S1	polymer	200	22749.8	2	UniProt (P0DTC2) Pfam (PF09408)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
4	G, H (F, G)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	branched		570.5	2	In PDB GlyTouCan (G21290RB)

Sequence modifications

M, E: 330 - 529 (UniProt: P0DTC2)

PDB	External Database	Details
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

Contents of the asymmetric unit

Polymers	Number of chains	6
	Total formula weight	96540.2
Branched	Number of molecules	2
	Total formula weight	1141.1
All*	Total formula weight	97681.3

*Water molecules are not included.