8BEV
Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD)
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A, C | Spike glycoprotein | polymer | 1267 | 140539.6 | 2 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
2 | B | immunoglobulin mu heavy chain | polymer | 167 | 17827.1 | 1 | Vicugna pacos (alpaca) | ||
3 | E, F, G | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 3 | In PDB GlyTouCan (G15407YE) | |||
4 | H | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
5 | C | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 1 | Chemie (NAG) |
Sequence modifications
A, C: 1 - 1208 (UniProt: P0DTC2)
PDB | External Database | Details |
---|---|---|
Gly 682 | Arg 682 | conflict |
Ser 683 | Arg 683 | conflict |
Ser 685 | Arg 685 | conflict |
Pro 817 | Phe 817 | conflict |
Pro 892 | Ala 892 | conflict |
Pro 899 | Ala 899 | conflict |
Pro 942 | Ala 942 | conflict |
Pro 986 | Lys 986 | conflict |
Pro 987 | Val 987 | conflict |
Gly 1209 | - | expression tag |
Ser 1210 | - | expression tag |
Gly 1211 | - | expression tag |
Tyr 1212 | - | expression tag |
Ile 1213 | - | expression tag |
Pro 1214 | - | expression tag |
Glu 1215 | - | expression tag |
Ala 1216 | - | expression tag |
Pro 1217 | - | expression tag |
Arg 1218 | - | expression tag |
Asp 1219 | - | expression tag |
Gly 1220 | - | expression tag |
Gln 1221 | - | expression tag |
Ala 1222 | - | expression tag |
Tyr 1223 | - | expression tag |
Val 1224 | - | expression tag |
Arg 1225 | - | expression tag |
Lys 1226 | - | expression tag |
Asp 1227 | - | expression tag |
Gly 1228 | - | expression tag |
Glu 1229 | - | expression tag |
Trp 1230 | - | expression tag |
Val 1231 | - | expression tag |
Leu 1232 | - | expression tag |
Leu 1233 | - | expression tag |
Ser 1234 | - | expression tag |
Thr 1235 | - | expression tag |
Phe 1236 | - | expression tag |
Leu 1237 | - | expression tag |
Gly 1238 | - | expression tag |
Arg 1239 | - | expression tag |
Ser 1240 | - | expression tag |
Leu 1241 | - | expression tag |
Glu 1242 | - | expression tag |
Val 1243 | - | expression tag |
Leu 1244 | - | expression tag |
Phe 1245 | - | expression tag |
Gln 1246 | - | expression tag |
Gly 1247 | - | expression tag |
Pro 1248 | - | expression tag |
Gly 1249 | - | expression tag |
His 1250 | - | expression tag |
His 1251 | - | expression tag |
His 1252 | - | expression tag |
His 1253 | - | expression tag |
His 1254 | - | expression tag |
His 1255 | - | expression tag |
His 1256 | - | expression tag |
His 1257 | - | expression tag |
Ser 1258 | - | expression tag |
Ala 1259 | - | expression tag |
Trp 1260 | - | expression tag |
Ser 1261 | - | expression tag |
His 1262 | - | expression tag |
Pro 1263 | - | expression tag |
Gln 1264 | - | expression tag |
Phe 1265 | - | expression tag |
Glu 1266 | - | expression tag |
Lys 1267 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 3 |
Total formula weight | 298906.3 | |
Branched | Number of molecules | 4 |
Total formula weight | 2184.0 | |
Non-Polymers* | Number of molecules | 1 |
Total formula weight | 221.2 | |
All* | Total formula weight | 301311.5 |