5VN3: Cryo-EM model of B41 SOSIP.664
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b. Determined by electron microscopy at 3.7 Å resolution. Released 12 Jul 2017.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organisms
- Homo sapiens, Human immunodeficiency virus 1
- Chains
- 15
- Atoms
- 23,727
- Mol. weight
- 456.06 kDa
- Ligands
- NAG
- Released
- 12 Jul 2017
Explore 5VN3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5VN3 contains 69 α-helices and 246 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, B and D: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 530-546 | 17 | |
| α-helix | 566-568 | 3 | |
| α-helix | 570-592 | 23 | |
| α-helix | 593-595 | 3 | |
| β-strand | 603 | 1 | 4 |
| α-helix | 608 | 1 | |
| β-strand | 609 | 1 | 4 |
| α-helix | 610-611 | 2 | |
| α-helix | 619-624 | 6 | |
| α-helix | 628-634 | 7 | |
| α-helix | 642-661 | 20 | |
Chains C, E and F: 3 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 18 |
| β-strand | 13-14 | 2 | 19 |
| β-strand | 28-29 | 2 | 18 |
| β-strand | 35 | 1 | 18 |
| β-strand | 39-40 | 2 | 20 |
| β-strand | 43-44 | 2 | 20 |
| β-strand | 45 | 1 | 17 |
| β-strand | 55-56 | 2 | 19 |
| α-helix | 59-61 | 3 | |
| β-strand | 69-71 | 3 | 19 |
| α-helix | 76-78 | 3 | |
| β-strand | 81-84 | 4 | 18 |
| β-strand | 92-97 | 6 | 18 |
| β-strand | 99-102 | 4 | 21 |
| β-strand | 112-115 | 4 | 22 |
| β-strand | 116-119 | 4 | 21 |
| α-helix | 120-121 | 2 | |
| β-strand | 127-129 | 3 | 23 |
| β-strand | 139 | 1 | 23 |
| β-strand | 145-149 | 5 | 22 |
| β-strand | 160-163 | 4 | 23 |
| β-strand | 166-168 | 3 | 23 |
Chains G, I and J: 10 helices, 40 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-45 | 11 | 4 |
| β-strand | 53-54 | 2 | 5 |
| β-strand | 55 | 1 | 6 |
| α-helix | 65-72 | 8 | |
| β-strand | 75 | 1 | 6 |
| α-helix | 76-78 | 3 | |
| β-strand | 84-85 | 2 | 7 |
| α-helix | 86 | 1 | |
| β-strand | 91 | 1 | 8 |
| α-helix | 101-112 | 12 | |
| β-strand | 120 | 1 | 9 |
| β-strand | 123 | 1 | 10 |
| β-strand | 126 | 1 | 11 |
| β-strand | 196 | 1 | 11 |
| β-strand | 199 | 1 | 10 |
| β-strand | 202 | 1 | 9 |
| β-strand | 215 | 1 | 12 |
| β-strand | 217-218 | 2 | 5 |
| β-strand | 223-227 | 5 | 7 |
| β-strand | 239 | 1 | 8 |
| β-strand | 243-245 | 3 | 7 |
| β-strand | 247 | 1 | 5 |
| β-strand | 251 | 1 | 12 |
| β-strand | 257 | 1 | 13 |
| α-helix | 264-266 | 3 | |
| β-strand | 271-273 | 3 | 14 |
| β-strand | 284-297 | 14 | 14 |
| β-strand | 329-332 | 4 | 14 |
| β-strand | 334 | 1 | 15 |
| α-helix | 335-349 | 15 | |
| β-strand | 357-361 | 4 | 16 |
| β-strand | 367 | 1 | 17 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-378 | 5 | 13 |
| β-strand | 381-385 | 5 | 13 |
| α-helix | 388-391 | 4 | |
| β-strand | 394 | 1 | 16 |
| β-strand | 413 | 1 | 15 |
| β-strand | 416-418 | 3 | 14 |
| β-strand | 420 | 1 | 13 |
| β-strand | 423-425 | 3 | 9 |
| β-strand | 432-434 | 3 | 9 |
| α-helix | 436-439 | 4 | |
| β-strand | 445-454 | 10 | 14 |
| β-strand | 457 | 1 | 16 |
| β-strand | 465-468 | 4 | 16 |
| β-strand | 470 | 1 | 14 |
| α-helix | 475-480 | 6 | |
| β-strand | 486-490 | 5 | 7 |
| β-strand | 491-499 | 9 | 4 |
Chains H, K and M: 1 helix, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 24 |
| β-strand | 18-23 | 6 | 24 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 25 |
| β-strand | 45-51 | 7 | 25 |
| β-strand | 57-59 | 3 | 25 |
| β-strand | 69-72 | 4 | 24 |
| β-strand | 77-82 | 6 | 24 |
| β-strand | 88-94 | 7 | 25 |
| β-strand | 102-103 | 2 | 25 |
| β-strand | 107-109 | 3 | 25 |
Chains L, N and O: 0 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 1 |
| β-strand | 11 | 1 | 2 |
| β-strand | 19-29 | 11 | 1 |
| β-strand | 33-38 | 6 | 3 |
| β-strand | 46-49 | 4 | 3 |
| β-strand | 53-54 | 2 | 3 |
| β-strand | 62-65 | 4 | 1 |
| β-strand | 68-75 | 8 | 1 |
| β-strand | 85-90 | 6 | 3 |
| β-strand | 102 | 1 | 3 |
| β-strand | 104 | 1 | 2 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 17b Fab light chain | L, N, O | protein | 214 | Homo sapiens | |
| Envelope glycoprotein gp160 | A, B, D | protein | 153 | Human immunodeficiency virus 1 | B3UEZ6 |
| Envelope glycoprotein gp160 | G, I, J | protein | 516 | Human immunodeficiency virus 1 | B3UES2 |
| T-cell surface glycoprotein CD4 | C, E, F | protein | 185 | Homo sapiens | P01730 (AlphaFold model) |
| 17b Fab heavy chain | H, K, M | protein | 229 | Homo sapiens | |
Sequence of entity 1 (L, N, O), FASTA
>5VN3_1 17b Fab light chain (chains L, N, O)
ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
Sequence of entity 2 (A, B, D), FASTA
>5VN3_2 Envelope glycoprotein gp160 (chains A, B, D)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD
Sequence of entity 3 (G, I, J), FASTA
>5VN3_3 Envelope glycoprotein gp160 (chains G, I, J)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV
Sequence of entity 4 (C, E, F), FASTA
>5VN3_4 T-cell surface glycoprotein CD4 (chains C, E, F)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASNT
Sequence of entity 5 (H, K, M), FASTA
>5VN3_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 | 24 |
Primary citation
Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Ozorowski, G., Pallesen, J., de Val, N. et al. Nature (2017) 547:360-363. DOI 10.1038/nature23010 · 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…
- 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
- 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…
- 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…
Browse structure collections
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