8OYU

Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '2 up 1 down' RBD conformation

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,Fibritin	polymer	1254	139470.0	3	UniProt (P0DTC2) UniProt (P10104) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein
2	E, D	H6 nanobody	polymer	126	13630.1	2		Lama glama
3	F, G, H, I, J...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	11	In PDB GlyTouCan (G42666HT)
4	C, A, B	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	15	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1205 (UniProt: P0DTC2)

PDB	External Database	Details
Val 67	Ala 67	variant
-	His 69	deletion
-	Val 70	deletion
Ile 93	Thr 95	variant
-	Gly 142	deletion
-	Val 143	deletion
-	Tyr 144	deletion
Asp 140	Tyr 145	variant
Ile 206	Asn 211	variant
Val 207	Leu 212	variant
Arg 208	Val 213	variant
Glu 209	Arg 214	variant
Pro 210	-	insertion
Glu 211	-	insertion
Asp 336	Gly 339	variant
Leu 368	Ser 371	variant
Pro 370	Ser 373	variant
Phe 372	Ser 375	variant
Asn 414	Lys 417	variant
Lys 437	Asn 440	variant
Ser 443	Gly 446	variant
Asn 474	Ser 477	variant
Lys 475	Thr 478	variant
Ala 481	Glu 484	variant
Lys 490	Gln 493	variant
Ser 493	Gly 496	variant
Arg 495	Gln 498	variant
Tyr 498	Asn 501	variant
His 502	Tyr 505	variant
Lys 544	Thr 547	variant
Gly 611	Asp 614	variant
Tyr 652	His 655	variant
Lys 676	Asn 679	variant
His 678	Pro 681	variant
Gly 679	Arg 682	engineered mutation
Ser 680	Arg 683	engineered mutation
Ser 682	Arg 685	engineered mutation
Lys 761	Asn 764	variant
Tyr 793	Asp 796	variant
Pro 814	Phe 817	engineered mutation
Lys 853	Asn 856	variant
Pro 889	Ala 892	engineered mutation
Pro 896	Ala 899	engineered mutation
Pro 939	Ala 942	engineered mutation
His 951	Gln 954	variant
Lys 966	Asn 969	variant
Phe 978	Leu 981	variant
Pro 983	Lys 986	engineered mutation
Pro 984	Val 987	engineered mutation
Gly 1206	-	linker
Ser 1207	-	linker

A, B, C: 1208 - 1234 (UniProt: P10104)

PDB	External Database	Details
Leu 1229	Phe 479	engineered mutation
Gly 1235	-	expression tag
Arg 1236	-	expression tag
Ser 1237	-	expression tag
Leu 1238	-	expression tag
Glu 1239	-	expression tag
Val 1240	-	expression tag
Leu 1241	-	expression tag
Phe 1242	-	expression tag
Gln 1243	-	expression tag
Gly 1244	-	expression tag
Pro 1245	-	expression tag
Gly 1246	-	expression tag
His 1247	-	expression tag
His 1248	-	expression tag
His 1249	-	expression tag
His 1250	-	expression tag
His 1251	-	expression tag
His 1252	-	expression tag
His 1253	-	expression tag
His 1254	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	5
	Total formula weight	445670.2
Branched	Number of molecules	11
	Total formula weight	4668.4
Non-Polymers*	Number of molecules	15
	Total formula weight	3318.1
All*	Total formula weight	453656.7

*Water molecules are not included.