8WPW

Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	S309 fab heavy chain	polymer	239	25747.7	1		Homo sapiens
2	B (B)	S309 fab light chain	polymer	215	23291.8	1		Homo sapiens
3	C (C)	CB6 fab mutant heavy chain	polymer	231	24862.9	1		Homo sapiens
4	D (D)	CB6 fab mutant light chain	polymer	216	23559.1	1		Homo sapiens
5	E (H)	S304 fab heavy chain	polymer	232	24930.7	1		Homo sapiens
6	F (L)	S304 fab light chain	polymer	216	23457.0	1		Homo sapiens
7	G (R)	Spike protein S1	polymer	229	25988.4	1	UniProt (P0DTC2) Pfam (PF09408)	Severe acute respiratory syndrome coronavirus 2
8	H (E)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	branched		570.5	1	In PDB GlyTouCan (G21290RB)

Sequence modifications

R: 319 - 541 (UniProt: P0DTC2)

PDB	External Database	Details
His 339	Gly 339	variant
Thr 346	Arg 346	variant
Ile 368	Leu 368	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
Pro 445	Val 445	variant
Ser 446	Gly 446	variant
Lys 460	Asn 460	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Pro 486	Phe 486	variant
Ser 490	Phe 490	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
His 542	-	expression tag
His 543	-	expression tag
His 544	-	expression tag
His 545	-	expression tag
His 546	-	expression tag
His 547	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	7
	Total formula weight	171837.6
Branched	Number of molecules	1
	Total formula weight	570.5
All*	Total formula weight	172408.2

*Water molecules are not included.