5FYK
Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade B JR-FL SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | B | JR-FL, GP41 ENV ECTODOMAIN | polymer | 161 | 18074.5 | 1 | UniProt (Q6BC19) Pfam (PF00517) UniProt (by SIFTS) (Q75760) In PDB | HUMAN IMMUNODEFICIENCY VIRUS 1 | |
2 | D | 35O22 | polymer | 243 | 26170.5 | 1 | HOMO SAPIENS (HUMAN) | ||
3 | E | 35O22 | polymer | 216 | 23318.8 | 1 | HOMO SAPIENS (HUMAN) | ||
4 | G | JR-FL, GP120 ENV ECTODOMAIN | polymer | 475 | 53732.0 | 1 | UniProt (Q75760) Pfam (PF00516) In PDB | HUMAN IMMUNODEFICIENCY VIRUS 1 | |
5 | H | PGT122 | polymer | 244 | 26465.9 | 1 | HOMO SAPIENS (HUMAN) | ||
6 | L | PGT122 | polymer | 213 | 22880.3 | 1 | HOMO SAPIENS (HUMAN) | ||
7 | U, V | VRC01 | polymer | 240 | 26153.3 | 2 | HOMO SAPIENS (HUMAN) | ||
8 | A | 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) | |||
9 | C | 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) | |||
10 | F, M | 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 | 2 | In PDB GlyTouCan (G68668TB) | |||
11 | I | alpha-D-mannopyranose-(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)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1235.1 | 1 | In PDB GlyTouCan (G91845HM) | |||
12 | J | 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 | K, 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 | 2 | In PDB GlyTouCan (G81315DD) | |||
14 | N | 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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1397.2 | 1 | In PDB GlyTouCan (G83582BK) | |||
15 | O | 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 | 1 | In PDB GlyTouCan (G22768VO) | |||
16 | P | alpha-D-mannopyranose-(1-2)-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 | 1397.2 | 1 | In PDB GlyTouCan (G33303XH) | |||
17 | Q | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(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)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1721.5 | 1 | In PDB GlyTouCan (G91704UR) | |||
18 | R, S | alpha-D-mannopyranose-(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)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1235.1 | 2 | In PDB GlyTouCan (G23799GS) | |||
19 | W | alpha-D-mannopyranose-(1-2)-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 | 1397.2 | 1 | In PDB GlyTouCan (G61846BY) | |||
20 | X | 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 | 1073.0 | 1 | In PDB GlyTouCan (G09724ZC) | |||
21 | a, Y | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 2 | In PDB GlyTouCan (G42666HT) | |||
22 | Z | 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 | 1 | In PDB GlyTouCan (G47410OF) | |||
23 | b | 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) | |||
24 | B, G, H | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 5 | Chemie (NAG) |
Sequence modifications
B: 512 - 664 (UniProt: Q6BC19)
G: 31 - 506 (UniProt: Q75760)
PDB | External Database | Details |
---|---|---|
Pro 559 | Ile 550 | engineered mutation |
Glu 563 | Gln 554 | conflict |
Cys 605 | Thr 596 | engineered mutation |
Gly 665 | - | expression tag |
Gly 666 | - | expression tag |
Leu 667 | - | expression tag |
Glu 668 | - | expression tag |
Val 669 | - | expression tag |
Leu 670 | - | expression tag |
Phe 671 | - | expression tag |
Gln 672 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Lys 168 | Glu 165 | engineered mutation |
Ile 430 | Val 421 | conflict |
Cys 459 | Gly 450 | engineered mutation |
Cys 501 | Ala 492 | engineered mutation |
Gly 507 | - | expression tag |
Arg 508 | - | expression tag |
Arg 509 | - | expression tag |
Arg 510 | - | expression tag |
Arg 511 | - | expression tag |
Arg 512 | - | expression tag |
Arg 513 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 8 |
Total formula weight | 222948.7 | |
Branched | Number of molecules | 20 |
Total formula weight | 22270.0 | |
Non-Polymers* | Number of molecules | 5 |
Total formula weight | 1106.0 | |
All* | Total formula weight | 246324.7 |