6CH7
XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 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) | Envelope glycoprotein gp41 | polymer | 153 | 17162.5 | 1 | UniProt (Q2N0S7) Pfam (PF00517) UniProt (by SIFTS) (Q2N0S5) | Human immunodeficiency virus 1 | Env polyprotein |
| 2 | B (D) | 35O22 Heavy Chain | polymer | 243 | 26171.5 | 1 | Homo sapiens (Human) | ||
| 3 | C (E) | 35O22 Light Chain | polymer | 216 | 23318.8 | 1 | Homo sapiens (Human) | ||
| 4 | D (G) | Envelope glycoprotein gp120 | polymer | 479 | 53737.8 | 1 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | Env polyprotein |
| 5 | E (Q) | BG18 Heavy Chain | polymer | 241 | 26158.4 | 1 | Homo sapiens (Human) | ||
| 6 | F (R) | BG18 Light Chain | polymer | 215 | 23021.4 | 1 | Homo sapiens (Human) | ||
| 7 | G (A) | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 894.8 | 1 | In PDB GlyTouCan (G00395TQ) | |||
| 8 | H (C) | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1422.3 | 1 | In PDB GlyTouCan (G61334IA) | |||
| 9 | I (F) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1422.3 | 1 | In PDB GlyTouCan (G17140UR) | |||
| 10 | J, L, O (H, J, M) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 3 | In PDB GlyTouCan (G15407YE) | |||
| 11 | K (I) | 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 | M (K) | 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 | 1235.1 | 1 | In PDB GlyTouCan (G84881ST) | |||
| 13 | N (L) | 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) | |||
| 14 | P (N) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 15 | Q (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 | 1 | In PDB GlyTouCan (G55220VL) | |||
| 16 | R (P) | alpha-D-mannopyranose-(1-6)-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 | 1235.1 | 1 | In PDB GlyTouCan (G51771NH) | |||
| 17 | S (S) | alpha-D-mannopyranose-(1-2)-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 (G60415BS) | |||
| 18 | T (T) | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 (G64261IK) | |||
| 19 | U, V, W (B, G) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 3 | Chemie (NAG) |
Sequence modifications
B: 512 - 664 (UniProt: Q2N0S7)
G: 31 - 511 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Cys 605 | Thr 602 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Thr 152 | Gly 143 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 501 | Ala 498 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 169570.5 | |
| Branched | Number of molecules | 14 |
| Total formula weight | 14082.8 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 663.6 | |
| All* | Total formula weight | 184316.9 |
