6MU6: HIV-1 BG505 SOSIP.664 Prefusion Env Trimer
Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-814508 in Complex with Human Antibodies 3H109L and 35O22 at 3.2 Angstrom. Determined by X-ray diffraction at 2.55 Å resolution. Released 16 Jan 2019.
- Method
- X-ray diffraction
- Resolution
- 2.55 Å
- Organisms
- Human immunodeficiency virus 1, Homo sapiens
- Chains
- 6
- Atoms
- 10,185
- Mol. weight
- 156.35 kDa
- Ligands
- JYV, NAG
- Released
- 16 Jan 2019
Explore 6MU6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6MU6 contains 35 α-helices and 111 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 | 537-541 | 5 | |
| 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, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 3 |
| β-strand | 19-25 | 7 | 3 |
| β-strand | 27 | 1 | 3 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-40 | 7 | 4 |
| β-strand | 46-51 | 6 | 4 |
| β-strand | 57-59 | 3 | 4 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72D | 10 | 3 |
| β-strand | 74-82 | 9 | 3 |
| β-strand | 88-94 | 7 | 4 |
| β-strand | 102-103 | 2 | 4 |
| β-strand | 107-108 | 2 | 4 |
Chain E: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 5 |
| β-strand | 9 | 1 | 6 |
| β-strand | 20-21 | 2 | 7 |
| β-strand | 24 | 1 | 5 |
| β-strand | 32-38 | 7 | 6 |
| β-strand | 45-49 | 5 | 6 |
| β-strand | 53-54 | 2 | 6 |
| α-helix | 55 | 1 | |
| β-strand | 62-66 | 5 | 7 |
| β-strand | 70 | 1 | 5 |
| β-strand | 71-75 | 5 | 7 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-91 | 7 | 6 |
| β-strand | 97-98 | 2 | 6 |
| β-strand | 102-103 | 2 | 6 |
Chain G: 12 helices, 41 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-40 | 6 | 2 |
| β-strand | 45-47 | 3 | 8 |
| β-strand | 53-56 | 4 | 9 |
| β-strand | 66-67 | 2 | 10 |
| α-helix | 71-73 | 3 | |
| β-strand | 75-76 | 2 | 9 |
| α-helix | 77-78 | 2 | |
| β-strand | 83-86 | 4 | 8 |
| β-strand | 91-94 | 4 | 11 |
| α-helix | 100-115 | 16 | |
| β-strand | 121 | 1 | 12 |
| α-helix | 123-125 | 3 | |
| β-strand | 129-133 | 5 | 13 |
| α-helix | 151-153 | 3 | |
| 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 |
| β-strand | 208-209 | 2 | 10 |
| β-strand | 215 | 1 | 14 |
| β-strand | 216-218 | 3 | 9 |
| α-helix | 219-220 | 2 | |
| β-strand | 223-228 | 6 | 8 |
| β-strand | 236-239 | 4 | 11 |
| β-strand | 242-245 | 4 | 8 |
| β-strand | 247 | 1 | 9 |
| β-strand | 251 | 1 | 14 |
| β-strand | 259-261 | 3 | 15 |
| β-strand | 271-273 | 3 | 15 |
| β-strand | 284 | 1 | 16 |
| β-strand | 285-308 | 24 | 15 |
| β-strand | 316-323 | 9 | 15 |
| β-strand | 330-334 | 5 | 15 |
| α-helix | 335-350 | 16 | |
| β-strand | 359-361 | 3 | 16 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-378 | 5 | 17 |
| β-strand | 381-385 | 5 | 17 |
| β-strand | 393-395 | 3 | 16 |
| β-strand | 413-417 | 5 | 15 |
| β-strand | 418-421 | 4 | 17 |
| β-strand | 423-425 | 3 | 12 |
| α-helix | 426 | 1 | |
| β-strand | 432-435 | 4 | 12 |
| α-helix | 437-440 | 4 | |
| β-strand | 441-452 | 12 | 15 |
| β-strand | 454-456 | 3 | 16 |
| β-strand | 466-470 | 5 | 16 |
| α-helix | 476-483 | 8 | |
| β-strand | 486-491 | 6 | 8 |
| β-strand | 494-499 | 6 | 2 |
Chain H: 6 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 18 |
| β-strand | 11-12 | 2 | 19 |
| β-strand | 18-25 | 8 | 18 |
| β-strand | 33-39 | 7 | 20 |
| β-strand | 45-51 | 7 | 20 |
| β-strand | 57-59 | 3 | 20 |
| α-helix | 64-66 | 3 | |
| β-strand | 67-69 | 3 | 18 |
| β-strand | 72 | 1 | 18 |
| β-strand | 77-82 | 6 | 18 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-100A | 14 | 20 |
| β-strand | 100J-101 | 10 | 20 |
| β-strand | 105-107 | 3 | 20 |
| β-strand | 108-109 | 2 | 19 |
| α-helix | 113-114 | 2 | |
| β-strand | 115 | 1 | 21 |
| β-strand | 118-122 | 5 | 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 | 157 | 1 | 23 |
| β-strand | 161-168 | 8 | 22 |
| β-strand | 174-183 | 10 | 22 |
| α-helix | 184-187 | 4 | |
| β-strand | 192-197 | 6 | 23 |
| α-helix | 199-201 | 3 | |
| β-strand | 205-209 | 5 | 23 |
Chain L: 7 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-14 | 6 | 24 |
| β-strand | 18-22 | 5 | 25 |
| β-strand | 31-38 | 8 | 24 |
| β-strand | 45-48 | 4 | 24 |
| β-strand | 62-63 | 2 | 25 |
| α-helix | 69-71 | 3 | |
| β-strand | 72-76 | 5 | 25 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-92 | 8 | 24 |
| β-strand | 97 | 1 | 20 |
| β-strand | 102-107 | 6 | 24 |
| α-helix | 109-111 | 3 | |
| β-strand | 112 | 1 | 26 |
| β-strand | 117-119 | 3 | 27 |
| α-helix | 120-122 | 3 | |
| α-helix | 123-127 | 5 | |
| β-strand | 131-140 | 10 | 27 |
| β-strand | 141 | 1 | 26 |
| β-strand | 145-151 | 7 | 28 |
| β-strand | 154-156 | 3 | 28 |
| β-strand | 160-162 | 3 | 27 |
| α-helix | 163-165 | 3 | |
| β-strand | 166-167 | 2 | 27 |
| β-strand | 173-181 | 9 | 27 |
| α-helix | 183-187 | 5 | |
| β-strand | 192-198 | 7 | 28 |
| β-strand | 201-207 | 7 | 28 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein gp160 | B | protein | 153 | Human immunodeficiency virus 1 | Q2N0S6 |
| 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 | 481 | Human immunodeficiency virus 1 | Q2N0S6 |
| 3H109L Fab heavy chain | H | protein | 244 | Homo sapiens | |
| 3H109L Fab light chain | L | protein | 217 | Homo sapiens | |
Sequence of entity 1 (B), FASTA
>6MU6_1 Envelope glycoprotein gp160 (chains B)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
Sequence of entity 2 (D), FASTA
>6MU6_2 35O22 scFv heavy chain portion (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVNMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSAST
Sequence of entity 3 (E), FASTA
>6MU6_3 35O22 scFv light chain portion (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQS
Sequence of entity 4 (G), FASTA
>6MU6_4 Envelope glycoprotein gp160 (chains G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R
Sequence of entity 5 (H), FASTA
>6MU6_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ
Sequence of entity 6 (L), FASTA
>6MU6_6 3H109L Fab light chain (chains L)
SVTSYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERF
SGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPMQWKMHKSYSCQVTHEGSTVEKTVAPTECS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| JYV | (2R)-{1-[{7-[2-({[3-(dimethylamino)propyl](methyl)amino}methyl)-1,3-thiazol-4-y… | C33 H39 N7 O3 S | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 10 |
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 Q2N0S6), best resolution first:
- 8TOX 2.3 Å, Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
- 6MTJ 2.34 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
- 6W03 2.4 Å, Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with…
- 6MTN 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
- 6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
- 8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
- 6MU7 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
- 6NNJ 2.6 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in…
- 8EUV 2.6 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
- 8T4K 2.6 Å, MD64 N332-GT5 sosip
- 8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB
- 8EUW 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB
Browse structure collections
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