Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map. Determined by electron microscopy at 3.8 Å resolution. Released 14 Nov 2018.
Explore 6MYY in 3D Show helices and sheets RCSB PDB PDBe
6MYY contains 102 α-helices and 192 β-strands across 9 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 35-40 | 6 | 1 |
| β-strand | 45-47 | 3 | 2 |
| β-strand | 53-55 | 3 | 3 |
| β-strand | 67 | 1 | 4 |
| β-strand | 75 | 1 | 3 |
| α-helix | 76-77 | 2 | |
| β-strand | 84-85 | 2 | 2 |
| β-strand | 91-94 | 4 | 5 |
| α-helix | 95-97 | 3 | |
| α-helix | 99-115 | 17 | |
| α-helix | 120 | 1 | |
| β-strand | 121 | 1 | 6 |
| β-strand | 129-132 | 4 | 7 |
| β-strand | 154-162 | 9 | 7 |
| β-strand | 169-177 | 9 | 7 |
| α-helix | 178-180 | 3 | |
| β-strand | 181-183 | 3 | 7 |
| β-strand | 190-193 | 4 | 7 |
| α-helix | 194-197 | 4 | |
| α-helix | 200-201 | 2 | |
| β-strand | 202-203 | 2 | 6 |
| α-helix | 204-205 | 2 | |
| β-strand | 209 | 1 | 4 |
| β-strand | 215 | 1 | 8 |
| β-strand | 216-218 | 3 | 3 |
| α-helix | 219-220 | 2 | |
| β-strand | 223-228 | 6 | 2 |
| β-strand | 236-239 | 4 | 5 |
| β-strand | 242-245 | 4 | 2 |
| β-strand | 247 | 1 | 3 |
| β-strand | 251 | 1 | 8 |
| β-strand | 256 | 1 | 9 |
| β-strand | 259-261 | 3 | 9 |
| α-helix | 264-266 | 3 | |
| β-strand | 271-273 | 3 | 9 |
| β-strand | 284-298 | 15 | 9 |
| β-strand | 302-312 | 9 | 7 |
| β-strand | 315-322 | 8 | 7 |
| β-strand | 329-333 | 5 | 9 |
| α-helix | 335-352 | 18 | |
| β-strand | 357-361 | 4 | 9 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-377 | 4 | 9 |
| β-strand | 382-385 | 4 | 9 |
| α-helix | 413 | 1 | |
| β-strand | 414-420 | 7 | 9 |
| β-strand | 423-424 | 2 | 6 |
| β-strand | 434-435 | 2 | 6 |
| α-helix | 436-438 | 3 | |
| β-strand | 443-456 | 14 | 9 |
| α-helix | 457 | 1 | |
| β-strand | 465-470 | 6 | 9 |
| α-helix | 476-480 | 5 | |
| α-helix | 483-485 | 3 | |
| β-strand | 486-491 | 6 | 2 |
| β-strand | 494-499 | 6 | 1 |
| α-helix | 524-527 | 4 | |
| β-strand | 529 | 1 | 10 |
| α-helix | 530-533 | 4 | |
| α-helix | 534-536 | 3 | |
| α-helix | 537-541 | 5 | |
| α-helix | 572-595 | 24 | |
| β-strand | 603-609 | 7 | 1 |
| α-helix | 610-611 | 2 | |
| α-helix | 619-620 | 2 | |
| α-helix | 621-625 | 5 | |
| β-strand | 627 | 1 | 10 |
| α-helix | 628-635 | 8 | |
| α-helix | 636-638 | 3 | |
| α-helix | 639-661 | 23 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 5-7 | 3 | 25 |
| β-strand | 10 | 1 | 26 |
| β-strand | 19-24 | 6 | 25 |
| β-strand | 34-38 | 5 | 26 |
| β-strand | 45-49 | 5 | 26 |
| β-strand | 53-54 | 2 | 26 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 25 |
| β-strand | 70-75 | 6 | 25 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 26 |
| β-strand | 97-98 | 2 | 26 |
| β-strand | 102-103 | 2 | 26 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-6 | 4 | 27 |
| β-strand | 10-11 | 2 | 28 |
| β-strand | 18-25 | 8 | 27 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 28 |
| β-strand | 45-52 | 8 | 28 |
| β-strand | 56-59 | 4 | 28 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72 | 6 | 27 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-82 | 6 | 27 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-94 | 7 | 28 |
| β-strand | 102-103 | 2 | 28 |
| β-strand | 107-110 | 4 | 28 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| 426c ds-sosip D3 | A, B, E | protein | 626 | Human immunodeficiency virus 1 | M4Q8P8, Q2N0S9 |
| VRC01GL light chain | C, F, L | protein | 229 | Homo sapiens | Q6PJF2 (AlphaFold model) |
| VRC01GL heavy chain | D, G, H | protein | 233 | Homo sapiens | S6C4S0 (AlphaFold model) |
>6MYY_1 426c DS-SOSIP D3 (chains A, B, E) AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVT ENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDN TTLGEIKNCSFDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTCTQ ACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNG SLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGD IRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCN TSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITCKSDITGLLLLRDGCN TANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAV FLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQA RVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNY TQIIYGLLEESQNQQEKNEQDLLALD
>6MYY_2 VRC01GL light chain (chains C, F, L) MGWSCIILFLVATATGVHSEIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPG QAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQYEFFGQGTKLE IKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTE QDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
>6MYY_3 VRC01GL heavy chain (chains D, G, H) QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY CQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKNSDYNWDFQHWGQGTLVTVS SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 12 |
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. Borst, A.J., Weidle, C.E., Gray, M.D. et al. Elife (2018) 7. DOI 10.7554/eLife.37688 · PubMed
Other PDB entries of the same protein (UniProt M4Q8P8), best resolution first:
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