Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2. Determined by electron microscopy at 2.4 Å resolution. Released 19 Feb 2025.
Explore 9DAK in 3D Show helices and sheets RCSB PDB PDBe
9DAK contains 59 α-helices and 28 β-strands across 2 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 |
|---|---|---|---|
| α-helix | 22-52 | 31 | |
| α-helix | 57-80 | 24 | |
| α-helix | 81-83 | 3 | |
| α-helix | 86-88 | 3 | |
| α-helix | 92-101 | 10 | |
| α-helix | 105-108 | 4 | |
| α-helix | 111-129 | 19 | |
| β-strand | 132-134 | 3 | 1 |
| β-strand | 142-144 | 3 | 1 |
| α-helix | 145-152 | 8 | |
| α-helix | 158-171 | 14 | |
| α-helix | 173-193 | 21 | |
| α-helix | 199-203 | 5 | |
| α-helix | 204-207 | 4 | |
| β-strand | 209 | 1 | 2 |
| β-strand | 217 | 1 | 2 |
| α-helix | 219-251 | 33 | |
| α-helix | 261 | 1 | |
| β-strand | 262-263 | 2 | 3 |
| α-helix | 264-266 | 3 | |
| α-helix | 276-278 | 3 | |
| α-helix | 279-282 | 4 | |
| α-helix | 294-299 | 6 | |
| α-helix | 304-316 | 13 | |
| α-helix | 321-324 | 4 | |
| α-helix | 327-330 | 4 | |
| β-strand | 332 | 1 | 4 |
| β-strand | 347-352 | 6 | 4 |
| β-strand | 355-359 | 5 | 4 |
| α-helix | 366-384 | 19 | |
| α-helix | 390-392 | 3 | |
| α-helix | 400-412 | 13 | |
| α-helix | 415-421 | 7 | |
| α-helix | 428-430 | 3 | |
| α-helix | 432-446 | 15 | |
| α-helix | 450-465 | 16 | |
| α-helix | 470-472 | 3 | |
| α-helix | 473-480 | 8 | |
| α-helix | 481-485 | 5 | |
| β-strand | 487-488 | 2 | 3 |
| α-helix | 499-502 | 4 | |
| α-helix | 504-507 | 4 | |
| α-helix | 514-532 | 19 | |
| α-helix | 539-541 | 3 | |
| α-helix | 548-558 | 11 | |
| α-helix | 566-574 | 9 | |
| α-helix | 582-587 | 6 | |
| α-helix | 589-599 | 11 | |
| β-strand | 617-621 | 5 | 5 |
| α-helix | 624-627 | 4 | |
| α-helix | 628-630 | 3 | |
| α-helix | 636-653 | 18 | |
| α-helix | 654-658 | 5 | |
| α-helix | 666-668 | 3 | |
| β-strand | 669-672 | 4 | 5 |
| β-strand | 679-684 | 6 | 5 |
| β-strand | 685-686 | 2 | 6 |
| β-strand | 689-693 | 5 | 6 |
| α-helix | 694-695 | 2 | |
| α-helix | 696-705 | 10 | |
| α-helix | 707-714 | 8 | |
| β-strand | 721-723 | 3 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 392 | 1 | 7 |
| α-helix | 394-396 | 3 | |
| α-helix | 397-399 | 3 | |
| β-strand | 401-403 | 3 | 8 |
| α-helix | 412-415 | 4 | |
| β-strand | 420-427 | 8 | 8 |
| α-helix | 431-435 | 5 | |
| β-strand | 444-448 | 5 | 8 |
| α-helix | 451-457 | 7 | |
| α-helix | 465-469 | 5 | |
| β-strand | 478-485 | 8 | 8 |
| α-helix | 488-490 | 3 | |
| β-strand | 492 | 1 | 7 |
| β-strand | 498-508 | 11 | 9 |
| β-strand | 515-521 | 7 | 9 |
| α-helix | 523-525 | 3 | |
| α-helix | 529-531 | 3 | |
| α-helix | 532-542 | 11 | |
| β-strand | 548-553 | 6 | 9 |
| β-strand | 558 | 1 | 10 |
| α-helix | 563 | 1 | |
| β-strand | 564 | 1 | 10 |
| α-helix | 565-566 | 2 | |
| β-strand | 567-574 | 8 | 9 |
| β-strand | 582-588 | 7 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| ACE2 | A | protein | 891 | Pipistrellus nathusii | Q56H28 (AlphaFold model) |
| Spike glycoprotein receptor binding domain | B | protein | 315 | Merbecovirus | A3EXD0 (AlphaFold model) |
>9DAK_1 ACE2 (chains A) MGGEGLRASPRRRPLLPLQPRGCPRGDGCLRGGRGRAGFGFWRVTGGSRASANHVHAFFF FLQLLGNVLVIVLSHHFGKEFATMPMGSLQPLATLYLLGMLVASVLAQSLTTEEKAREFL DKFNSEAENWSHESALASWDYNTNINDKNAQKMNEADSKWSAFYKEHSKLAQGFPLQEIQ NSTIKLQLQILQQNGSSVLTAEKSKRLSTILTTMSTIYSTGKVCNPNNPQQCFTLSGLED IMEKSKDYHQRLWIWEGWRSEVGKQLRPLYEEYVALKNEMARGNNYKDYGDYWRGDYETE GGDGYNYSRNHLIEDVDRIFLEIKPLYEQLHAYVRAKLMNAYPSRISPTGCLPAHLLGDM WGRFWTNLYNLTVPFEKKQNIDVTDTMKKQSWDAEKIFKEAEKFYLSVGLHNMTPEFWNN SMLTEPSDGRQVVCHPTAWDLGKNDFRIKMCTKVTMDDFLTAHHEMGHIQYDMAYAKQPY LLRNGANEGFHEAVGEIMSLSAATPKHLKDLGLLAQNYPEDYETEINFLLKQALNIVGTL PFTYMLEKWRWMVFEGKIPKEQWMEKWWEMKREIVGVVEPLPHDETYCDPASLFHVANDY SFIRYFTRTILEFQFQEALCQIANHTGPLHKCDISNSTEAGKQLKNMLELGKSKPWTFAL EQIARTKEMDAKPLLNYFKPLFSWLKELNGNSVGWSADWSPYSEQSIKVRISLKSALGEK AYEWNDNEMYLFRSSVAYAMRVYFLKVKNETIPFRAEDVWVSDEKIRVSFKFFVTSPTNV SDIIPRSEVEDAIRMSRGRINDAFRLDDKTLEFLGIQPTLGPPYQPPVTGTGGGSWSHPQ FEKGGGSGGGSGGSAWSHPQFEKGGGGSDYKDHDGDYKDHDIDYKDDDDKL
>9DAK_2 Spike glycoprotein receptor binding domain (chains B) MGILPSPGMPALLSLVSLLSVLLMGCVAETGTYSVSSFEARPQGSFVESVYEGNECDFTK LFRGPVPQPYEFGRLVFTNCNYNFTKLLSYFQVDAFECKKVTPESIATGCYSSLTVDWFA YRVADKSDLLPGSSSDLQRFNYKPTYAHPTCLISAYTDLSALGGSNPTNYTLLTNCYGCV GQPPKRTCLEEFPSFVEAGYRPKPSCARIGMQGHASGNETYTAVVTNNELDSVGDPIWRM GVAQTKEPSVTDKAELAFFVSVQIDSQSSSVCPLGSPKLVPRGSSSGGSGLNDIFEAQKI EWHEGGSHHHHHHHH
Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses. Ma, C.B., Liu, C., Park, Y.J. et al. Cell (2025) 188:1693-1710.e18. DOI 10.1016/j.cell.2024.12.031 · PubMed
Other PDB entries of the same protein (UniProt Q56H28 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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