5FYL
Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (B) | BG505 GP120 ENV ECTODOMAIN | polymer | 153 | 17146.5 | 1 | UniProt (Q2N0S6) Pfam (PF00517) | HUMAN IMMUNODEFICIENCY VIRUS 1 | |
| 2 | B (D) | 35O22 ANTIBODY FAB HEAVY CHAIN | polymer | 243 | 26170.5 | 1 | HOMO SAPIENS (HUMAN) | ||
| 3 | C (E) | 35O22 ANTIBODY FAB LIGHT CHAIN | polymer | 216 | 23318.8 | 1 | HOMO SAPIENS (HUMAN) | ||
| 4 | D (G) | BG505 GP120 ENV ECTODOMAIN | polymer | 481 | 54064.3 | 1 | UniProt (Q2N0S6) Pfam (PF00516) | HUMAN IMMUNODEFICIENCY VIRUS 1 | |
| 5 | E (H) | PGT122 ANTIBODY FAB HEAVY CHAIN | polymer | 244 | 26465.9 | 1 | HOMO SAPIENS (HUMAN) | ||
| 6 | F (L) | PGT122 ANTIBODY FAB LIGHT CHAIN | polymer | 213 | 22880.3 | 1 | HOMO SAPIENS (HUMAN) | ||
| 7 | G, T (A, T) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 2 | In PDB GlyTouCan (G15407YE) | |||
| 8 | H, J (C, I) | 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) | |||
| 9 | I (F) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 10 | K (J) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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 | 1559.4 | 1 | In PDB GlyTouCan (G83161QT) | |||
| 11 | L (K) | 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) | |||
| 12 | M (M) | 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 | 1 | In PDB GlyTouCan (G09724ZC) | |||
| 13 | N, P (N, P) | 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) | |||
| 14 | O (O) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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 | 1397.2 | 1 | In PDB GlyTouCan (G33303XH) | |||
| 15 | Q (Q) | 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) | |||
| 16 | R (R) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 (G80966KZ) | |||
| 17 | S (S) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | 1721.5 | 1 | In PDB GlyTouCan (G91704UR) | |||
| 18 | U, V (U, 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 | 2 | In PDB GlyTouCan (G56014GC) | |||
| 19 | W (W) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-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 (G02763QD) | |||
| 20 | X (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 | 1 | In PDB GlyTouCan (G81315DD) | |||
| 21 | AA, BA, Y, Z (G, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 4 | Chemie (NAG) |
Sequence modifications
B: 512 - 664 (UniProt: Q2N0S6)
G: 31 - 508 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Pro 559 | Ile 556 | engineered mutation |
| Cys 605 | Thr 602 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Asn 332 | Thr 330 | engineered mutation |
| Cys 501 | Ala 498 | engineered mutation |
| Arg 509 | - | expression tag |
| Arg 510 | - | expression tag |
| Arg 511 | - | expression tag |
| Arg 512 | - | expression tag |
| Arg 513 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 170046.3 | |
| Branched | Number of molecules | 18 |
| Total formula weight | 19637.6 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 884.8 | |
| All* | Total formula weight | 190568.7 |
