6N1W
Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody DFPH-a.15 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, I, Q (2, C, c) | Envelope glycoprotein gp120 | polymer | 473 | 52987.0 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 2 | B, K, S (3, H, h) | DFPH-a.15 heavy chain | polymer | 224 | 24004.8 | 3 | Macaca mulatta | ||
| 3 | C, L, T (4, L, l) | DFPH-a.15 Light chain | polymer | 212 | 22962.3 | 3 | Macaca mulatta | ||
| 4 | D, M, U (5, M, m) | PGT122 Heavy chain | polymer | 132 | 14838.7 | 3 | Homo sapiens (human) | ||
| 5 | E, N, V (6, N, n) | PGT122 Light chain | polymer | 105 | 11423.5 | 3 | Homo sapiens (human) | ||
| 6 | F, P, X (7, R, r) | VRC03 Light chain | polymer | 102 | 11386.8 | 3 | Homo sapiens (human) | ||
| 7 | G, O, W (8, Q, q) | VRC03 Heavy chain | polymer | 128 | 14506.3 | 3 | Homo sapiens (human) | ||
| 8 | H, J, R (A, D, d) | Envelope glycoprotein gp41 | polymer | 153 | 17162.5 | 3 | UniProt (Q2N0S7) Pfam (PF00517) | Human immunodeficiency virus 1 | |
| 9 | AA, AB, BA, BB, CA... (F, t, G, u, I...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 21 | In PDB GlyTouCan (G42666HT) | |||
| 10 | HA, HB, KA, KB, MA... (S, 0, V, AA, 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 | 9 | In PDB GlyTouCan (G81315DD) | |||
| 11 | DA, DB, QA (J, w, b) | 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 | 3 | In PDB GlyTouCan (G22768VO) | |||
| 12 | GA, GB, TA (P, z, g) | 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) | |||
| 13 | IA, IB, VA (T, 1, j) | 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)]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 | 1559.4 | 3 | In PDB GlyTouCan (G68668TB) | |||
| 14 | LB, MB, NB, OB, PB... (2, C, c) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 9 | Chemie (NAG) |
Sequence modifications
2, C, c: 31 - 505 (UniProt: Q2N0S6)
A, D, d: 512 - 664 (UniProt: Q2N0S7)
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 433 | Ala 430 | conflict |
| Cys 501 | Ala 498 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Cys 605 | Thr 602 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 24 |
| Total formula weight | 507816.0 | |
| Branched | Number of molecules | 39 |
| Total formula weight | 24820.8 | |
| Non-Polymers* | Number of molecules | 9 |
| Total formula weight | 1990.9 | |
| All* | Total formula weight | 534627.7 |
