7VQ0
Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86
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 | 1247 | 138155.0 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | S glycoprotein,E2,Peplomer protein |
| 2 | D, E, F (D, E, F) | Neutralizing nanobody P86 | polymer | 122 | 13432.9 | 3 | Vicugna pacos | ||
| 3 | AA, BA, CA, G, H... (a, b, c, G, H...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 17 | In PDB GlyTouCan (G42666HT) | |||
| 4 | DA, N, V (d, N, V) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 3 | In PDB GlyTouCan (G21290RB) | |||
| 5 | EA, FA, O, P, W... (e, f, O, P, W...) | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 6 | In PDB GlyTouCan (G62182OO) | |||
| 6 | AB, BB, CB, DB, EB... (C, A, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 30 | Chemie (NAG) |
Sequence modifications
A, B, C: 1 - 1208 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Gly 614 | Asp 614 | engineered mutation |
| Gly 682 | Arg 682 | engineered mutation |
| Ser 683 | Arg 683 | engineered mutation |
| Ser 685 | Arg 685 | engineered mutation |
| Pro 986 | Lys 986 | engineered mutation |
| Pro 987 | Val 987 | engineered mutation |
| 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 |
| Ser 1239 | - | expression tag |
| His 1240 | - | expression tag |
| His 1241 | - | expression tag |
| His 1242 | - | expression tag |
| His 1243 | - | expression tag |
| His 1244 | - | expression tag |
| His 1245 | - | expression tag |
| His 1246 | - | expression tag |
| His 1247 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 454763.8 | |
| Branched | Number of molecules | 26 |
| Total formula weight | 12445.7 | |
| Non-Polymers* | Number of molecules | 30 |
| Total formula weight | 6636.2 | |
| All* | Total formula weight | 473845.7 |
