9D3D
Cryo-EM structure of PGT145 R100aS Fab bound to HIV-1 BG505 DS-SOSIP.664 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, B, C (C, A, B) | HIV-1 BG505 DS-SOSIP gp120 | polymer | 481 | 54086.3 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 2 | D, E, F (c, a, b) | BG505 DS-SOSIP glycoprotein gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) UniProt (by SIFTS) (D0PUM0) | Human immunodeficiency virus 1 | |
| 3 | G (H) | PGT145 R100aS Heavy Chain | polymer | 244 | 26323.2 | 1 | Homo sapiens (human) | ||
| 4 | H (L) | PGT145 Light Chain | polymer | 219 | 23953.8 | 1 | Homo sapiens (human) | ||
| 5 | AA, CA, DA, EA, FA... (X, Z, d, e, f...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 22 | In PDB GlyTouCan (G42666HT) | |||
| 6 | HA, L (h, G) | 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 | 2 | In PDB GlyTouCan (G22768VO) | |||
| 7 | LA, M (l, I) | 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 | 2 | In PDB GlyTouCan (G81315DD) | |||
| 8 | BA, P, QA, T, Z (Y, M, q, Q, W) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 5 | In PDB GlyTouCan (G15407YE) | |||
| 9 | PA, RA, S (p, r, P) | 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 | U (R) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | 1 | In PDB GlyTouCan (G07617FP) | |||
| 11 | MA (m) | beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 1 | In PDB GlyTouCan (G44266EX) | |||
| 12 | AB, BB, CB, DB, EB... (A, B, c, a, b...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 24 | Chemie (NAG) | |||
| 13 | FB (A) | PHOSPHATE ION | non-polymer | 95.0 | 1 | Chemie (PO4) |
Sequence modifications
C, A, B: 31 - 508 (UniProt: Q2N0S6)
c, a, b: 512 - 664 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 433 | Ala 430 | 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 | engineered mutation |
| Cys 605 | Thr 602 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 8 |
| Total formula weight | 263975.4 | |
| Branched | Number of molecules | 36 |
| Total formula weight | 20629.1 | |
| Non-Polymers* | Number of molecules | 25 |
| Total formula weight | 5404.0 | |
| All* | Total formula weight | 290008.5 |
