6OT1
Cryo-EM structure of vaccine-elicited antibody 0PV-b.01 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 (B, O, D) | Envelope glycoprotein gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) | Human immunodeficiency virus 1 (HIV-1) | |
| 2 | B, J, R (G, E, P) | BG505 gp120 | polymer | 480 | 53987.2 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | Env polyprotein |
| 3 | C, K, S (H, A, M) | 0PV-b.01 heavy | polymer | 230 | 24430.4 | 3 | Macaca mulatta | ||
| 4 | D, L, T (L, C, N) | 0PV-b.01 light | polymer | 219 | 23843.5 | 3 | Macaca mulatta | ||
| 5 | E, M, U (m, F, Q) | PGT122 heavy | polymer | 235 | 25434.7 | 3 | Homo sapiens | ||
| 6 | F, N, V (n, I, R) | PGT122 light | polymer | 213 | 22880.3 | 3 | Homo sapiens | ||
| 7 | G, O, W (q, J, S) | VRC03 heavy | polymer | 233 | 25248.4 | 3 | Homo sapiens | ||
| 8 | H, P, X (r, K, T) | VRC03 light | polymer | 209 | 23146.8 | 3 | Homo sapiens | ||
| 9 | AB, BA, CA, CB, DA... (0, X, Y, 2, Z...) | 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 | BB, DB, JA, MA, NB... (1, 3, f, i, DA...) | 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 | 9 | In PDB GlyTouCan (G22768VO) | |||
| 11 | AA, EB, IA, KA, MB... (W, 4, e, g, CA...) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 9 | In PDB GlyTouCan (G15407YE) | |||
| 12 | EA, IB, TA (a, 8, t) | 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 | 3 | In PDB GlyTouCan (G81315DD) | |||
| 13 | HA, LB, WA (d, BA, w) | 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 | 3 | In PDB GlyTouCan (G56014GC) | |||
| 14 | AC, BC, CC, RB, SB... (P, B, G, O, E...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 12 | Chemie (NAG) |
Sequence modifications
B, O, D: 512 - 664 (UniProt: Q2N0S6)
G, E, P: 31 - 511 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Pro 559 | Ile 556 | engineered mutation |
| Cys 605 | Thr 602 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 433 | Ala 430 | conflict |
| Cys 501 | Ala 498 | conflict |
| Gly 506 | Val 503 | conflict |
| Arg 507 | Gly 504 | conflict |
| Arg 509 | Glu 506 | conflict |
| Arg 510 | Lys 507 | conflict |
| Arg 512 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 24 |
| Total formula weight | 648353.4 | |
| Branched | Number of molecules | 45 |
| Total formula weight | 27853.6 | |
| Non-Polymers* | Number of molecules | 12 |
| Total formula weight | 2654.5 | |
| All* | Total formula weight | 678861.5 |
