8TNG
Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody R27 targeting the CD4-binding site
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C, E (A, C, E) | HIV-1 BG505 DS-SOSIP gp120 | polymer | 481 | 54086.3 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 2 | B, D, F (B, D, F) | Envelope glycoproteiHIV-1 BG505 DS-SOSIP gp41n gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) | Human immunodeficiency virus 1 | Env polyproten |
| 3 | G, H, I (H, I, J) | CD4-binding site targeting nanobody R27 | polymer | 121 | 12984.4 | 3 | Lama glama (llama) | ||
| 4 | AA, BA, CA, DA, EA... (a, b, c, d, e...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 19 | In PDB GlyTouCan (G42666HT) | |||
| 5 | K (K) | 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) | |||
| 6 | S, Z (S, Z) | 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) | |||
| 7 | AB, BB, CB, DB, EB... (E, A, B, C) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 27 | Chemie (NAG) |
Sequence modifications
A, C, E: 31 - 508 (UniProt: Q2N0S6)
B, D, F: 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 | conflict |
| Cys 605 | Thr 602 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 9 |
| Total formula weight | 252651.6 | |
| Branched | Number of molecules | 22 |
| Total formula weight | 10147.5 | |
| Non-Polymers* | Number of molecules | 27 |
| Total formula weight | 5972.6 | |
| All* | Total formula weight | 268771.7 |
