7TXD
Cryo-EM structure of BG505 SOSIP HIV-1 Env trimer in complex with CD4 receptor (D1D2) and broadly neutralizing darpin bnD.9
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C, E (A, C, E) | Envelope glycoprotein gp120 | polymer | 481 | 54064.3 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 2 | B, D, F (B, D, F) | Envelope glycoprotein gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) | Human immunodeficiency virus 1 | Env polyprotein |
| 3 | G, H, I (G, H, I) | T-cell surface glycoprotein CD4 | polymer | 185 | 20503.3 | 3 | UniProt (P01730) Pfam (PF00047) Pfam (PF05790) | Homo sapiens (human) | T-cell surface antigen T4/Leu-3 |
| 4 | J, K, L (J, K, L) | Broadly neutralizing darpin bnd.9 | polymer | 196 | 21214.9 | 3 | synthetic construct | ||
| 5 | BA, M (b, M) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1235.1 | 2 | In PDB GlyTouCan (G46836GH) | |||
| 6 | CA, EA, FA, N, P... (c, e, f, N, P...) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 8 | In PDB GlyTouCan (G15407YE) | |||
| 7 | AA, DA, GA, HA, O... (a, d, g, h, O...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 11 | In PDB GlyTouCan (G42666HT) | |||
| 8 | V (V) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 910.8 | 1 | In PDB GlyTouCan (G22768VO) | |||
| 9 | AB, BB, CB, DB, EB... (D, E, A, F, B...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 30 | Chemie (NAG) |
Sequence modifications
A, C, E: 31 - 508 (UniProt: Q2N0S6)
B, D, F: 512 - 664 (UniProt: Q2N0S6)
G, H, I: 1 - 183 (UniProt: P01730)
| PDB | External Database | Details |
|---|---|---|
| Asn 332 | Thr 330 | conflict |
| Cys 501 | Ala 498 | conflict |
| Arg 509 | - | expression tag |
| Arg 510 | - | expression tag |
| Arg 511 | - | expression tag |
| Arg 512 | - | expression tag |
| Arg 513 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Pro 559 | Ile 556 | conflict |
| Cys 605 | Thr 602 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Asn 184 | - | expression tag |
| Thr 185 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 338786.7 | |
| Branched | Number of molecules | 22 |
| Total formula weight | 12741.8 | |
| Non-Polymers* | Number of molecules | 30 |
| Total formula weight | 6636.2 | |
| All* | Total formula weight | 358164.8 |
