7N28
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 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, F, G | Envelope glycoprotein gp120 | polymer | 478 | 54234.8 | 3 | UniProt (I6NF57) Pfam (PF00516) In PDB | Human immunodeficiency virus 1 | |
| 2 | C, J, S | 3BNC117 antibody heavy chain | polymer | 226 | 24656.5 | 3 | Homo sapiens | ||
| 3 | D, K, U | 3BNC117 antibody light chain | polymer | 206 | 23022.7 | 3 | Homo sapiens | ||
| 4 | X | J033 antibody heavy chain | polymer | 230 | 24473.4 | 1 | Macaca mulatta | ||
| 5 | Y | J033 antibody light chain | polymer | 214 | 23267.9 | 1 | Macaca mulatta | ||
| 6 | M, B, N | Envelope glycoprotein gp41 | polymer | 170 | 19174.8 | 3 | UniProt (I6NF57) Pfam (PF00517) In PDB | Human immunodeficiency virus 1 | Env polyprotein |
| 7 | a, b, c, f, g... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 25 | In PDB GlyTouCan (G42666HT) | |||
| 8 | L | 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 | e, 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 | 2 | In PDB GlyTouCan (G55220VL) | |||
| 10 | 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 | d | 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 | 1 | In PDB GlyTouCan (G22573RC) | |||
| 12 | k | 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 | 1073.0 | 1 | In PDB GlyTouCan (G34442SS) | |||
| 13 | m | 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 | 1 | In PDB GlyTouCan (G56014GC) | |||
| 14 | n | 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 | 1 | In PDB GlyTouCan (G81315DD) | |||
| 15 | A, K, U, D, M... | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 40 | Chemie (NAG) | |||
| 16 | A, F | PHOSPHATE ION | non-polymer | 95.0 | 3 | Chemie (PO4) | |||
| 17 | S, X | alpha-D-mannopyranose | non-polymer | 180.2 | 2 | Chemie (MAN) |
Sequence modifications
A, F, G: 31 - 511 (UniProt: I6NF57)
M, B, N: 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 |
| Gly 665 | - | expression tag |
| Ser 666 | - | expression tag |
| Ala 667 | - | expression tag |
| Pro 668 | - | expression tag |
| Thr 669 | - | expression tag |
| Lys 670 | - | expression tag |
| Ala 671 | - | expression tag |
| Lys 672 | - | expression tag |
| Arg 673 | - | expression tag |
| Arg 674 | - | expression tag |
| Val 675 | - | expression tag |
| Val 676 | - | expression tag |
| Gln 677 | - | expression tag |
| Arg 678 | - | expression tag |
| Glu 679 | - | expression tag |
| Lys 680 | - | expression tag |
| Arg 681 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 14 |
| Total formula weight | 411007.5 | |
| Branched | Number of molecules | 33 |
| Total formula weight | 18707.3 | |
| Non-Polymers* | Number of molecules | 45 |
| Total formula weight | 9493.5 | |
| All* | Total formula weight | 439208.4 |
