9BER
Cryo-EM structure of the HIV-1 JR-FL IDL Env trimer in complex with PGT122 Fab
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 (G, A, F) | Envelope glycoprotein gp120 | polymer | 477 | 53686.9 | 3 | UniProt (Q75760) Pfam (PF00516) | Human immunodeficiency virus 1 (HIV-1) | |
| 2 | B, D, F (B, C, I) | Envelope glycoprotein gp41 | polymer | 153 | 17227.5 | 3 | UniProt (Q6BC19) Pfam (PF00517) | Human immunodeficiency virus 1 (HIV-1) | |
| 3 | G, I, K (H, D, J) | PGT122 heavy chain | polymer | 132 | 14838.7 | 3 | Homo sapiens (human) | ||
| 4 | H, J, L (L, E, K) | PGT122 light chain | polymer | 105 | 11423.5 | 3 | Homo sapiens (human) | ||
| 5 | BA, CA, M, N, P... (b, c, M, N, P...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 12 | In PDB GlyTouCan (G42666HT) | |||
| 6 | AA, O, U (a, O, U) | 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) | |||
| 7 | DA, R, X (d, R, X) | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 | 1073.0 | 3 | In PDB GlyTouCan (G09724ZC) | |||
| 8 | AB, BB, CB, DB, EA... (A, G, C, F, B...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 45 | Chemie (NAG) | |||
| 9 | FB (A) | SULFATE ION | non-polymer | 96.1 | 1 | Chemie (SO4) |
Sequence modifications
G, A, F: 31 - 505 (UniProt: Q75760)
B, C, I: 512 - 664 (UniProt: Q6BC19)
| PDB | External Database | Details |
|---|---|---|
| Cys 113 | Asp 112 | conflict |
| Lys 168 | Glu 165 | conflict |
| Asn 197 | Asp 194 | conflict |
| Thr 236 | Lys 233 | conflict |
| Gly 431 | - | insertion |
| Cys 431 | - | insertion |
| Gly 432 | Lys 423 | conflict |
| Val 506 | - | expression tag |
| Gly 507 | - | expression tag |
| Arg 508 | - | expression tag |
| 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 550 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 291530.2 | |
| Branched | Number of molecules | 18 |
| Total formula weight | 10557.8 | |
| Non-Polymers* | Number of molecules | 46 |
| Total formula weight | 10050.4 | |
| All* | Total formula weight | 312138.4 |
