7MXD
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, D, E (A, F, G) | Envelope glycoprotein gp120 | polymer | 478 | 54234.8 | 3 | UniProt (I6NF57) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 2 | B, F, H (C, J, S) | 3BNC117 antibody heavy chain | polymer | 226 | 24656.5 | 3 | Homo sapiens | ||
| 3 | C, G, I (D, K, U) | 3BNC117 antibody light chain | polymer | 206 | 23022.7 | 3 | Homo sapiens | ||
| 4 | J (X) | J038 antibody heavy chain | polymer | 228 | 24413.3 | 1 | Macaca mulatta | ||
| 5 | K (Y) | J038 antibody light chain | polymer | 214 | 23187.7 | 1 | Macaca mulatta | ||
| 6 | L, M, N (B, I, H) | Envelope glycoprotein gp41 | polymer | 153 | 17218.5 | 3 | UniProt (I6NF57) Pfam (PF00517) | Human immunodeficiency virus 1 | |
| 7 | AA, BA, CA, FA, GA... (a, b, c, f, g...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 27 | In PDB GlyTouCan (G42666HT) | |||
| 8 | R (N) | alpha-D-mannopyranose-(1-2)-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 | 1397.2 | 1 | In PDB GlyTouCan (G83582BK) | |||
| 9 | EA, MA, PA, S (e, m, p, O) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | 1235.1 | 4 | In PDB GlyTouCan (G55220VL) | |||
| 10 | U (Q) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 1 | In PDB GlyTouCan (G15407YE) | |||
| 11 | DA, OA (d, o) | 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 | 2 | In PDB GlyTouCan (G56014GC) | |||
| 12 | AB, AC, BB, BC, CB... (A, K, U, B, D...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 38 | Chemie (NAG) | |||
| 13 | FB, HB, IB (A, F) | PHOSPHATE ION | non-polymer | 95.0 | 3 | Chemie (PO4) |
Sequence modifications
A, F, G: 31 - 511 (UniProt: I6NF57)
B, I, H: 512 - 664 (UniProt: I6NF57)
| PDB | External Database | Details |
|---|---|---|
| Ala 31 | Ser 30 | conflict |
| Glu 32 | Asp 31 | conflict |
| Pro 124 | His 123 | conflict |
| Leu 179 | Thr 179 | conflict |
| Cys 201 | Ile 200 | conflict |
| Thr 358 | Lys 355 | conflict |
| Thr 400 | Gly 397 | conflict |
| Cys 433 | Ala 425 | conflict |
| Cys 501 | Ala 495 | conflict |
| Arg 509 | Glu 503 | conflict |
| Arg 510 | Lys 504 | conflict |
| Arg 512 | - | expression tag |
| Arg 513 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Asn 535 | Ile 529 | conflict |
| Pro 556 | Leu 550 | conflict |
| Pro 559 | Ile 553 | conflict |
| Glu 588 | Lys 582 | conflict |
| Val 589 | Asp 583 | conflict |
| Cys 605 | Thr 599 | conflict |
| Phe 651 | Asn 645 | conflict |
| Ile 655 | Arg 649 | conflict |
| Val 658 | Lys 652 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 14 |
| Total formula weight | 404998.2 | |
| Branched | Number of molecules | 35 |
| Total formula weight | 20529.0 | |
| Non-Polymers* | Number of molecules | 41 |
| Total formula weight | 8690.8 | |
| All* | Total formula weight | 434218.0 |
