6X5B: Envelope glycoprotein gp120
Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52. Determined by electron microscopy at 3.6 Å resolution. Released 21 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organisms
- Human immunodeficiency virus 1, Homo sapiens
- Chains
- 15
- Atoms
- 20,232
- Mol. weight
- 452.53 kDa
- Ligands
- NAG, UOV
- Released
- 21 Oct 2020
Explore 6X5B in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6X5B contains 93 α-helices and 186 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 J: 11 helices, 28 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 | 66-68 | 3 | |
| α-helix | 70-73 | 4 | |
| β-strand | 75 | 1 | 3 |
| α-helix | 76-77 | 2 | |
| β-strand | 84-85 | 2 | 2 |
| β-strand | 91-94 | 4 | 4 |
| α-helix | 100-113 | 14 | |
| β-strand | 120-123 | 4 | 5 |
| β-strand | 199-202 | 4 | 5 |
| β-strand | 215-218 | 4 | 3 |
| α-helix | 219-220 | 2 | |
| β-strand | 223-228 | 6 | 2 |
| β-strand | 236-239 | 4 | 4 |
| β-strand | 242-245 | 4 | 2 |
| β-strand | 247 | 1 | 3 |
| β-strand | 251 | 1 | 3 |
| β-strand | 259-261 | 3 | 6 |
| β-strand | 271-273 | 3 | 6 |
| α-helix | 283 | 1 | |
| β-strand | 284-298 | 15 | 6 |
| β-strand | 328-333 | 6 | 6 |
| α-helix | 335-352 | 18 | |
| β-strand | 367 | 1 | 7 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-378 | 5 | 6 |
| β-strand | 381-385 | 5 | 6 |
| β-strand | 414-421 | 8 | 6 |
| β-strand | 423-425 | 3 | 5 |
| β-strand | 432-434 | 3 | 5 |
| α-helix | 436-439 | 4 | |
| β-strand | 443-455 | 13 | 6 |
| α-helix | 468 | 1 | |
| β-strand | 469-470 | 2 | 6 |
| α-helix | 476-483 | 8 | |
| β-strand | 486-491 | 6 | 2 |
| β-strand | 494-499 | 6 | 1 |
Chains B, E and K: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 517-523 | 7 | |
| α-helix | 524-527 | 4 | |
| β-strand | 529 | 1 | 8 |
| α-helix | 530-545 | 16 | |
| α-helix | 551-553 | 3 | |
| α-helix | 562-564 | 3 | |
| α-helix | 566-592 | 27 | |
| α-helix | 593-596 | 4 | |
| β-strand | 603-609 | 7 | 1 |
| α-helix | 610-611 | 2 | |
| α-helix | 619-625 | 7 | |
| β-strand | 627 | 1 | 8 |
| α-helix | 628-634 | 7 | |
| α-helix | 636-638 | 3 | |
| α-helix | 639-657 | 19 | |
Chains C, G and N: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 7 |
| β-strand | 12-17 | 6 | 11 |
| β-strand | 26-30 | 5 | 7 |
| β-strand | 35-40 | 6 | 7 |
| β-strand | 43-46 | 4 | 7 |
| β-strand | 55-56 | 2 | 11 |
| α-helix | 59-64 | 6 | |
| β-strand | 66-71 | 6 | 11 |
| α-helix | 76-78 | 3 | |
| β-strand | 81-86 | 6 | 7 |
| β-strand | 92-95 | 4 | 7 |
Chains F, L and M: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 22 |
| β-strand | 10 | 1 | 23 |
| β-strand | 19-25 | 7 | 22 |
| β-strand | 33-38 | 6 | 23 |
| β-strand | 45-49 | 5 | 23 |
| α-helix | 53 | 1 | |
| β-strand | 54 | 1 | 23 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 22 |
| β-strand | 70-75 | 6 | 22 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 23 |
| β-strand | 97-98 | 2 | 23 |
| β-strand | 102-103 | 2 | 23 |
Chains H, I and O: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 12 |
| β-strand | 10-11 | 2 | 13 |
| β-strand | 18-25 | 8 | 12 |
| α-helix | 29-31 | 3 | |
| β-strand | 32-39 | 8 | 13 |
| β-strand | 46-52 | 7 | 13 |
| β-strand | 56-59 | 4 | 13 |
| β-strand | 67-72 | 6 | 12 |
| β-strand | 77-82 | 6 | 12 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-96 | 9 | 13 |
| α-helix | 100-100B | 3 | |
| β-strand | 102-103 | 2 | 13 |
| β-strand | 107-110 | 4 | 13 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein gp120 | A, D, J | protein | 524 | Human immunodeficiency virus 1 | B3UES2 |
| Envelope glycoprotein gp41 | B, E, K | protein | 153 | Human immunodeficiency virus 1 | B3UEZ6 |
| 17b Fab light chain | F, L, M | protein | 214 | Homo sapiens | |
| T-cell surface glycoprotein CD4 | C, G, N | protein | 208 | Homo sapiens | P01730 (AlphaFold model) |
| 17b Fab heavy chain | H, I, O | protein | 229 | Homo sapiens | |
Sequence of entity 1 (A, D, J), FASTA
>6X5B_1 Envelope glycoprotein gp120 (chains A, D, J)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR
Sequence of entity 2 (B, E, K), FASTA
>6X5B_2 Envelope glycoprotein gp41 (chains B, E, K)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD
Sequence of entity 3 (F, L, M), FASTA
>6X5B_3 17b Fab light chain (chains F, L, M)
ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
Sequence of entity 4 (C, G, N), FASTA
>6X5B_4 T-cell surface glycoprotein CD4 (chains C, G, N)
METDTLLLWVLLLWVPGSTGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQ
GSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGL
TANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT
VLQNQKKVEFKIDIVVLAGGSGHHHHHH
Sequence of entity 5 (H, I, O), FASTA
>6X5B_5 17b Fab heavy chain (chains H, I, O)
QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 27 |
| UOV | N-(4'-methyl[1,1'-biphenyl]-4-yl)-1-oxa-7-azaspiro[3.5]nonane-7-carboxamide | C21 H24 N2 O2 | 3 |
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…
- 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
- 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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