6MUG: HIV-1 B41 SOSIP.664 Prefusion Env Trimer
Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.8 Angstrom. Determined by X-ray diffraction at 2.95 Å resolution. Released 16 Jan 2019.
- Method
- X-ray diffraction
- Resolution
- 2.95 Å
- Organisms
- Human immunodeficiency virus 1, Homo sapiens
- Chains
- 6
- Atoms
- 9,963
- Mol. weight
- 156.24 kDa
- Ligands
- JYS, NAG
- Released
- 16 Jan 2019
Explore 6MUG in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6MUG contains 30 α-helices and 112 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain B: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 529 | 1 | 1 |
| α-helix | 530-533 | 4 | |
| α-helix | 539-542 | 4 | |
| α-helix | 570-594 | 25 | |
| β-strand | 603-609 | 7 | 2 |
| α-helix | 620-623 | 4 | |
| β-strand | 627 | 1 | 1 |
| α-helix | 628-634 | 7 | |
| α-helix | 639-660 | 22 | |
Chain D: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 3 |
| β-strand | 20-25 | 6 | 3 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-40 | 7 | 4 |
| β-strand | 41 | 1 | 5 |
| β-strand | 43 | 1 | 5 |
| β-strand | 45-51 | 7 | 4 |
| β-strand | 57-59 | 3 | 4 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-71 | 5 | 3 |
| β-strand | 77-82 | 6 | 3 |
| β-strand | 88-94 | 7 | 4 |
| β-strand | 102-103 | 2 | 4 |
| β-strand | 107-108 | 2 | 4 |
Chain E: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-6 | 2 | 6 |
| β-strand | 11-12 | 2 | 7 |
| β-strand | 19-21 | 3 | 8 |
| β-strand | 23-24 | 2 | 6 |
| β-strand | 32-38 | 7 | 7 |
| β-strand | 45-49 | 5 | 7 |
| β-strand | 53-54 | 2 | 7 |
| α-helix | 55 | 1 | |
| β-strand | 62-66 | 5 | 8 |
| β-strand | 71-75 | 5 | 8 |
| α-helix | 80-82 | 3 | |
| β-strand | 84-91 | 8 | 7 |
| β-strand | 97-98 | 2 | 7 |
| β-strand | 102-105 | 4 | 7 |
Chain G: 9 helices, 40 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-40 | 6 | 2 |
| β-strand | 45-47 | 3 | 9 |
| β-strand | 53-56 | 4 | 10 |
| β-strand | 75-76 | 2 | 10 |
| β-strand | 83-85 | 3 | 9 |
| β-strand | 91-94 | 4 | 11 |
| α-helix | 99-115 | 17 | |
| α-helix | 120 | 1 | |
| β-strand | 121 | 1 | 12 |
| β-strand | 129-132 | 4 | 13 |
| β-strand | 154-162 | 9 | 13 |
| β-strand | 169-177 | 9 | 13 |
| α-helix | 178-180 | 3 | |
| β-strand | 181-183 | 3 | 13 |
| β-strand | 190-193 | 4 | 13 |
| β-strand | 200-203 | 4 | 12 |
| α-helix | 204-205 | 2 | |
| β-strand | 215 | 1 | 14 |
| β-strand | 216-218 | 3 | 10 |
| α-helix | 219-220 | 2 | |
| β-strand | 223-228 | 6 | 9 |
| β-strand | 236-239 | 4 | 11 |
| β-strand | 242-245 | 4 | 9 |
| β-strand | 247 | 1 | 10 |
| β-strand | 251 | 1 | 14 |
| β-strand | 257 | 1 | 15 |
| β-strand | 259 | 1 | 15 |
| β-strand | 261 | 1 | 13 |
| β-strand | 271-273 | 3 | 13 |
| β-strand | 284-308 | 25 | 13 |
| β-strand | 316-323 | 9 | 13 |
| β-strand | 330-334 | 5 | 13 |
| α-helix | 335-348 | 14 | |
| β-strand | 359-361 | 3 | 16 |
| β-strand | 374-378 | 5 | 13 |
| β-strand | 381-386 | 6 | 13 |
| β-strand | 394-395 | 2 | 16 |
| β-strand | 413-414 | 2 | 13 |
| β-strand | 417-421 | 5 | 13 |
| β-strand | 423-425 | 3 | 12 |
| β-strand | 432-435 | 4 | 12 |
| α-helix | 437-440 | 4 | |
| β-strand | 441-454 | 14 | 13 |
| β-strand | 456 | 1 | 16 |
| β-strand | 466-468 | 3 | 16 |
| α-helix | 476-480 | 5 | |
| α-helix | 483-485 | 3 | |
| β-strand | 488-491 | 4 | 9 |
| β-strand | 494-499 | 6 | 2 |
Chain H: 6 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 17 |
| β-strand | 11-12 | 2 | 18 |
| β-strand | 18 | 1 | 19 |
| β-strand | 22-25 | 4 | 17 |
| β-strand | 33-39 | 7 | 20 |
| β-strand | 46-51 | 6 | 20 |
| β-strand | 57-59 | 3 | 20 |
| β-strand | 72 | 1 | 17 |
| β-strand | 77 | 1 | 17 |
| β-strand | 82 | 1 | 19 |
| α-helix | 84-86 | 3 | |
| β-strand | 89-100A | 13 | 20 |
| β-strand | 100J-101 | 10 | 20 |
| β-strand | 105-106 | 2 | 20 |
| β-strand | 108-109 | 2 | 18 |
| α-helix | 113-114 | 2 | |
| β-strand | 115 | 1 | 21 |
| β-strand | 119-122 | 4 | 22 |
| β-strand | 133-143 | 11 | 22 |
| β-strand | 144 | 1 | 21 |
| β-strand | 149-152 | 4 | 23 |
| α-helix | 153-155 | 3 | |
| β-strand | 161 | 1 | 22 |
| α-helix | 163-165 | 3 | |
| β-strand | 174-183 | 10 | 22 |
| α-helix | 185-187 | 3 | |
| β-strand | 193-198 | 6 | 23 |
| α-helix | 199-201 | 3 | |
| β-strand | 203-208 | 6 | 23 |
Chain L: 5 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-14 | 5 | 24 |
| β-strand | 18-22 | 5 | 25 |
| β-strand | 31 | 1 | 26 |
| β-strand | 34-38 | 5 | 27 |
| β-strand | 45-48 | 4 | 27 |
| β-strand | 62-64 | 3 | 25 |
| β-strand | 72-76 | 5 | 25 |
| β-strand | 85-89 | 5 | 27 |
| β-strand | 92 | 1 | 26 |
| β-strand | 103-107 | 5 | 24 |
| α-helix | 109-111 | 3 | |
| β-strand | 117-119 | 3 | 28 |
| α-helix | 120-122 | 3 | |
| α-helix | 123-127 | 5 | |
| β-strand | 133-136 | 4 | 28 |
| β-strand | 137-140 | 4 | 29 |
| β-strand | 145-151 | 7 | 30 |
| β-strand | 154-155 | 2 | 30 |
| β-strand | 160-162 | 3 | 28 |
| α-helix | 163-165 | 3 | |
| β-strand | 166-167 | 2 | 29 |
| β-strand | 173-175 | 3 | 29 |
| β-strand | 177-179 | 3 | 28 |
| α-helix | 183-188 | 6 | |
| β-strand | 192-198 | 7 | 30 |
| β-strand | 201-204 | 4 | 30 |
| β-strand | 207 | 1 | 30 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein gp160 | B | protein | 153 | Human immunodeficiency virus 1 | B3UEZ6 |
| 35O22 scFv heavy chain portion | D | protein | 134 | Homo sapiens | |
| 35O22 scFv light chain portion | E | protein | 114 | Homo sapiens | |
| Envelope glycoprotein gp160 | G | protein | 489 | Human immunodeficiency virus 1 | B3UES2 |
| 3H109L Fab heavy chain | H | protein | 244 | Homo sapiens | |
| 3H109L Fab light chain | L | protein | 217 | Homo sapiens | |
Sequence of entity 1 (B), FASTA
>6MUG_1 Envelope glycoprotein gp160 (chains B)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD
Sequence of entity 2 (D), FASTA
>6MUG_2 35O22 scFv heavy chain portion (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVNMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSAST
Sequence of entity 3 (E), FASTA
>6MUG_3 35O22 scFv light chain portion (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQS
Sequence of entity 4 (G), FASTA
>6MUG_4 Envelope glycoprotein gp160 (chains G)
AAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVT
ENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDW
EKMETGEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTS
VITQACPKVSFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQL
LLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATG
DIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGE
FFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIR
CSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRR
VVQRRRRRR
Sequence of entity 5 (H), FASTA
>6MUG_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ
Sequence of entity 6 (L), FASTA
>6MUG_6 3H109L Fab light chain (chains L)
SVTSYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERF
SGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPMQWKMHKSYSCQVTHEGSTVEKTVAPTECS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| JYS | 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-… | C21 H17 Br F N3 O3 | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 14 |
Primary citation
Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry. Lai, Y.T., Wang, T., O'Dell, S. et al. Nat Commun (2019) 10:47-47. DOI 10.1038/s41467-018-07851-1 · PubMed
Other PDB entries of the same protein (UniProt B3UEZ6), best resolution first:
- 6MUF 2.91 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human…
- 6OKP 3.28 Å, B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody…
- 6OPN 3.5 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35
- 6OPO 3.5 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
- 5VN8 3.6 Å, Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain…
- 6X5B 3.6 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule…
- 5VN3 3.7 Å, Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen…
- 6OPP 3.7 Å, Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
- 6OPQ 3.8 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG
- 6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
- 6X5C 4.04 Å, Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52
- 6EDU 4.06 Å, B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody…
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