6OPQ: Envelope glycoprotein gp160
CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG. Determined by electron microscopy at 3.8 Å resolution. Released 21 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organisms
- Human immunodeficiency virus 1, Homo sapiens
- Chains
- 15
- Atoms
- 20,877
- Mol. weight
- 456.45 kDa
- Ligands
- NAG
- Released
- 21 Oct 2020
Explore 6OPQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6OPQ contains 75 α-helices and 198 β-strands across 15 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.
Chains A, D and E: 11 helices, 31 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-40 | 6 | 1 |
| β-strand | 45-47 | 3 | 2 |
| β-strand | 53-56 | 4 | 3 |
| α-helix | 65-73 | 9 | |
| β-strand | 75 | 1 | 3 |
| α-helix | 76-77 | 2 | |
| β-strand | 84-85 | 2 | 2 |
| β-strand | 91-93 | 3 | 4 |
| α-helix | 100-113 | 14 | |
| β-strand | 120-125 | 6 | 5 |
| β-strand | 197-202 | 6 | 5 |
| β-strand | 215-218 | 4 | 3 |
| α-helix | 219-220 | 2 | |
| β-strand | 224-228 | 5 | 2 |
| β-strand | 237-239 | 3 | 4 |
| β-strand | 242-245 | 4 | 2 |
| β-strand | 247 | 1 | 3 |
| α-helix | 248-250 | 3 | |
| β-strand | 251 | 1 | 3 |
| β-strand | 259-261 | 3 | 6 |
| α-helix | 264-266 | 3 | |
| β-strand | 271 | 1 | 6 |
| β-strand | 286-297 | 12 | 6 |
| β-strand | 329-334 | 6 | 6 |
| α-helix | 335-352 | 18 | |
| β-strand | 357-361 | 4 | 7 |
| β-strand | 367 | 1 | 8 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-378 | 5 | 6 |
| β-strand | 381-385 | 5 | 6 |
| α-helix | 388-390 | 3 | |
| β-strand | 394-395 | 2 | 7 |
| β-strand | 413-421 | 9 | 6 |
| β-strand | 423-425 | 3 | 5 |
| β-strand | 432-434 | 3 | 5 |
| α-helix | 436-439 | 4 | |
| β-strand | 444-452 | 9 | 6 |
| β-strand | 455-456 | 2 | 7 |
| β-strand | 465-469 | 5 | 7 |
| α-helix | 475-483 | 9 | |
| β-strand | 486-491 | 6 | 2 |
| β-strand | 494-499 | 6 | 1 |
Chains B, F and G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 523-525 | 3 | |
| β-strand | 529 | 1 | 11 |
| α-helix | 530-545 | 16 | |
| α-helix | 566-592 | 27 | |
| α-helix | 593-596 | 4 | |
| β-strand | 603-604 | 2 | 1 |
| α-helix | 619-625 | 7 | |
| β-strand | 627 | 1 | 11 |
| α-helix | 628-634 | 7 | |
| α-helix | 639-660 | 22 | |
Chains C, I and J: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-5 | 4 | 8 |
| β-strand | 12-14 | 3 | 12 |
| β-strand | 17 | 1 | 13 |
| β-strand | 26-29 | 4 | 8 |
| β-strand | 35-40 | 6 | 8 |
| β-strand | 43-46 | 4 | 8 |
| β-strand | 55-56 | 2 | 12 |
| α-helix | 59-64 | 6 | |
| β-strand | 66 | 1 | 13 |
| β-strand | 69-71 | 3 | 12 |
| α-helix | 76-78 | 3 | |
| β-strand | 80-86 | 7 | 8 |
| β-strand | 89-96 | 8 | 8 |
Chains H, K and M: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-6 | 2 | 14 |
| β-strand | 10-12 | 3 | 15 |
| β-strand | 18-23 | 6 | 14 |
| α-helix | 29-31 | 3 | |
| β-strand | 32-39 | 8 | 15 |
| β-strand | 46-52 | 7 | 15 |
| β-strand | 56-59 | 4 | 15 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72 | 6 | 14 |
| β-strand | 77-82 | 6 | 14 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-96 | 9 | 15 |
| α-helix | 100-100B | 3 | |
| β-strand | 102-103 | 2 | 15 |
| β-strand | 107-111 | 5 | 15 |
Chains L, N and O: 1 helix, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 9 |
| β-strand | 10-12 | 3 | 10 |
| β-strand | 19-29 | 11 | 9 |
| β-strand | 33-38 | 6 | 10 |
| β-strand | 45-49 | 5 | 10 |
| β-strand | 53-54 | 2 | 10 |
| β-strand | 62-75 | 14 | 9 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 10 |
| β-strand | 97 | 1 | 10 |
| β-strand | 102-105 | 4 | 10 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein gp160 | A, D, E | protein | 524 | Human immunodeficiency virus 1 | B3UES2 |
| 17b Fab light chain | L, N, O | protein | 214 | Homo sapiens | |
| Envelope glycoprotein gp41 | B, F, G | protein | 153 | Human immunodeficiency virus 1 | B3UEZ6 |
| T-cell surface glycoprotein CD4 | C, I, J | protein | 208 | Homo sapiens | P01730 (AlphaFold model) |
| 17b Fab heavy chain | H, K, M | protein | 229 | Homo sapiens | |
Sequence of entity 1 (A, D, E), FASTA
>6OPQ_1 Envelope glycoprotein gp160 (chains A, D, E)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR
Sequence of entity 2 (L, N, O), FASTA
>6OPQ_2 17b Fab light chain (chains L, N, O)
ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
Sequence of entity 3 (B, F, G), FASTA
>6OPQ_3 Envelope glycoprotein gp41 (chains B, F, G)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD
Sequence of entity 4 (C, I, J), FASTA
>6OPQ_4 T-cell surface glycoprotein CD4 (chains C, I, J)
METDTLLLWVLLLWVPGSTGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQ
GSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGL
TANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT
VLQNQKKVEFKIDIVVLAGGSGHHHHHH
Sequence of entity 5 (H, K, M), FASTA
>6OPQ_5 17b Fab heavy chain (chains H, K, M)
QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 9 |
Primary citation
A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide. Ozorowski, G., Torres, J.L., Santos-Martins, D. et al. Cell Rep (2020) 33:108428-108428. DOI 10.1016/j.celrep.2020.108428 · PubMed
Other PDB entries of the same protein (UniProt B3UES2), best resolution first:
- 6MUF 2.91 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human…
- 6MUG 2.95 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
- 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
- 6MCO 3.53 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23…
- 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
- 6MDT 3.82 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63…
- 6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
Browse structure collections
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