9YYV

SARS-CoV-2 spike trimer in the early fusion intermediate conformation bound to the VN01H1 Fab (S2 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, B, C (A, B, C)	Spike glycoprotein	polymer	1281	141609.0	3	UniProt (P0DTC2)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, E, F, G, H... (A, B, C)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	15	Chemie (NAG)

Sequence modifications

A, B, C: 14 - 1211 (UniProt: P0DTC2)

PDB	External Database	Details
Met -18	-	initiating methionine
Gly -17	-	expression tag
Ile -16	-	expression tag
Leu -15	-	expression tag
Pro -14	-	expression tag
Ser -13	-	expression tag
Pro -12	-	expression tag
Gly -11	-	expression tag
Met -10	-	expression tag
Pro -9	-	expression tag
Ala -8	-	expression tag
Leu -7	-	expression tag
Leu -6	-	expression tag
Ser -5	-	expression tag
Leu -4	-	expression tag
Val -3	-	expression tag
Ser -2	-	expression tag
Leu -1	-	expression tag
Leu 0	-	expression tag
Ser 1	-	expression tag
Val 2	-	expression tag
Leu 3	-	expression tag
Leu 4	-	expression tag
Met 5	-	expression tag
Gly 6	-	expression tag
Cys 7	-	expression tag
Val 8	-	expression tag
Ala 9	-	expression tag
Glu 10	-	expression tag
Thr 11	-	expression tag
Gly 12	-	expression tag
Thr 13	-	expression tag
Gly 614	Asp 614	variant
Ser 682	Arg 682	engineered mutation
Gly 683	Arg 683	engineered mutation
Gly 1212	-	expression tag
Ser 1213	-	expression tag
Gly 1214	-	expression tag
Arg 1215	-	expression tag
Glu 1216	-	expression tag
Asn 1217	-	expression tag
Leu 1218	-	expression tag
Tyr 1219	-	expression tag
Phe 1220	-	expression tag
Gln 1221	-	expression tag
Gly 1222	-	expression tag
Gly 1223	-	expression tag
Gly 1224	-	expression tag
Gly 1225	-	expression tag
Ser 1226	-	expression tag
Gly 1227	-	expression tag
Tyr 1228	-	expression tag
Ile 1229	-	expression tag
Pro 1230	-	expression tag
Glu 1231	-	expression tag
Ala 1232	-	expression tag
Pro 1233	-	expression tag
Arg 1234	-	expression tag
Asp 1235	-	expression tag
Gly 1236	-	expression tag
Gln 1237	-	expression tag
Ala 1238	-	expression tag
Tyr 1239	-	expression tag
Val 1240	-	expression tag
Arg 1241	-	expression tag
Lys 1242	-	expression tag
Asp 1243	-	expression tag
Gly 1244	-	expression tag
Glu 1245	-	expression tag
Trp 1246	-	expression tag
Val 1247	-	expression tag
Leu 1248	-	expression tag
Leu 1249	-	expression tag
Ser 1250	-	expression tag
Thr 1251	-	expression tag
Phe 1252	-	expression tag
Leu 1253	-	expression tag
Gly 1254	-	expression tag
His 1255	-	expression tag
His 1256	-	expression tag
His 1257	-	expression tag
His 1258	-	expression tag
His 1259	-	expression tag
His 1260	-	expression tag
His 1261	-	expression tag
His 1262	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	424827.0
Non-Polymers*	Number of molecules	15
	Total formula weight	3318.1
All*	Total formula weight	428145.1

*Water molecules are not included.