9PNN
Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E, I (B, A, F) | Envelope glycoprotein BG505 DS-SOSIP gp41 | polymer | 153 | 17162.5 | 3 | UniProt (Q2N0S7) Pfam (PF00517) | Human immunodeficiency virus 1 | |
| 2 | B, F, J (G, C, I) | Envelope glycoprotein BG505 DS-SOSIP gp120 | polymer | 473 | 52987.0 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 3 | C, G, K (H, D, J) | antibody J601-A6 heavy chain | polymer | 234 | 25058.9 | 3 | Macaca mulatta | ||
| 4 | D, H, L (L, E, K) | antibody J601-A6 light chain | polymer | 215 | 23630.1 | 3 | Macaca mulatta | ||
| 5 | BA, M, QA (b, M, q) | 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 | 748.7 | 3 | In PDB GlyTouCan (G22573RC) | |||
| 6 | CA, EA, JA, N, P... (c, e, j, N, P...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 9 | In PDB GlyTouCan (G42666HT) | |||
| 7 | DA, O, SA (d, O, s) | 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 | 3 | In PDB GlyTouCan (G22768VO) | |||
| 8 | AA, AB, CB, DB, EB... (a, 0, 2, 3, 4...) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 24 | In PDB GlyTouCan (G15407YE) | |||
| 9 | GA, R, VA (g, R, v) | 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 | 1073.0 | 3 | In PDB GlyTouCan (G56014GC) | |||
| 10 | BB, MA, X (1, m, X) | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 748.7 | 3 | In PDB GlyTouCan (G81315DD) | |||
| 11 | FB, GB, HB, IB, JB... (B, G, A, C, F...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 15 | Chemie (NAG) |
Sequence modifications
B, A, F: 512 - 664 (UniProt: Q2N0S7)
G, C, I: 31 - 505 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Cys 605 | Thr 602 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | engineered mutation |
| Asn 332 | Thr 330 | engineered mutation |
| Cys 433 | Ala 430 | engineered mutation |
| Cys 501 | Ala 498 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 356515.6 | |
| Branched | Number of molecules | 45 |
| Total formula weight | 28340.1 | |
| Non-Polymers* | Number of molecules | 15 |
| Total formula weight | 3318.1 | |
| All* | Total formula weight | 388173.7 |
