7UGO
Cryo-EM structure of BG24 inferred germline Fabs with mature CDR3s and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B, C | Envelope glycoprotein gp120 | polymer | 466 | 52322.4 | 3 | UniProt (Q2N0S5) Pfam (PF00516) In PDB | Human immunodeficiency virus 1 | Env polyprotein |
| 2 | D, E, F | Envelope glycoprotein gp41 | polymer | 129 | 14676.7 | 3 | Pfam (PF00517) UniProt (by SIFTS) (Q2N0S5) In PDB | Human immunodeficiency virus 1 | |
| 3 | M, N, O | 10-1074 Fab heavy chain | polymer | 133 | 14791.4 | 3 | Homo sapiens | ||
| 4 | P, Q, R | 10-1074 Fab light chain | polymer | 107 | 11701.0 | 3 | Homo sapiens | ||
| 5 | G, H, I | BG24 inferred germline Fab with mature CDR3s heavy chain | polymer | 125 | 13697.3 | 3 | Homo sapiens | ||
| 6 | J, K, L | BG24 inferred germline Fab with mature CDR3s light chain | polymer | 106 | 11180.2 | 3 | Homo sapiens | ||
| 7 | g, S | 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) | |||
| 8 | T | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)]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 | |||
| 9 | b, c, d, f, i... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 12 | In PDB GlyTouCan (G42666HT) | |||
| 10 | e, X | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | branched | 342.3 | 2 | In PDB GlyTouCan (G53402KW) | |||
| 11 | Z | 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) | |||
| 12 | a | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 (G94559IJ) | |||
| 13 | h | 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) | |||
| 14 | C, D, E, F, A... | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 21 | Chemie (NAG) | |||
| 15 | B, C, A | alpha-D-mannopyranose | non-polymer | 180.2 | 4 | Chemie (MAN) |
Sequence modifications
A, B, C: 32 - 506 (UniProt: Q2N0S5)
| PDB | External Database | Details |
|---|---|---|
| Lys 64 | Glu 63 | conflict |
| Arg 169 | Lys 160 | conflict |
| His 173 | Tyr 164 | conflict |
| Ala 174 | Ser 165 | conflict |
| Lys 178 | Arg 169 | conflict |
| Ile 181 | Val 172 | conflict |
| Pro 183 | Gln 174 | conflict |
| - | Gly 180 | deletion |
| - | Asn 181 | deletion |
| - | Arg 182 | deletion |
| - | Ser 183 | deletion |
| - | Asn 184 | deletion |
| - | Asn 185 | deletion |
| - | Ser 186 | deletion |
| Thr 189 | Lys 188 | conflict |
| Ser 190 | Glu 189 | conflict |
| Ala 199 | Ser 198 | conflict |
| Asp 276 | Asn 275 | conflict |
| Arg 278 | Thr 277 | conflict |
| Trp 316 | Ala 313 | conflict |
| Asn 332 | Thr 330 | conflict |
| Asp 386 | Asn 384 | conflict |
| Asp 462 | Asn 459 | conflict |
| Ser 471 | Gly 468 | conflict |
| Cys 501 | Ala 498 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 18 |
| Total formula weight | 355107.4 | |
| Branched | Number of molecules | 20 |
| Total formula weight | 11890.9 | |
| Non-Polymers* | Number of molecules | 25 |
| Total formula weight | 5366.0 | |
| All* | Total formula weight | 372364.3 |
