SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab region. Determined by electron microscopy at 3.51 Å resolution. Released 21 Aug 2024.
Explore 8ZHG in 3D Show helices and sheets RCSB PDB PDBe
8ZHG contains 13 α-helices and 36 β-strands across 3 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 | 334 | 1 | |
| β-strand | 335 | 1 | 1 |
| α-helix | 336 | 1 | |
| α-helix | 338-342 | 5 | |
| β-strand | 354-358 | 5 | 2 |
| β-strand | 362 | 1 | 1 |
| β-strand | 374-379 | 6 | 2 |
| α-helix | 384-386 | 3 | |
| β-strand | 394-403 | 10 | 2 |
| α-helix | 404-406 | 3 | |
| α-helix | 407-410 | 4 | |
| β-strand | 432-437 | 6 | 2 |
| β-strand | 448 | 1 | 3 |
| β-strand | 454 | 1 | 4 |
| α-helix | 471-473 | 3 | |
| β-strand | 492 | 1 | 4 |
| α-helix | 494-496 | 3 | |
| β-strand | 497 | 1 | 3 |
| α-helix | 503-505 | 3 | |
| β-strand | 507-516 | 10 | 2 |
| β-strand | 525 | 1 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 5 |
| β-strand | 6 | 1 | 6 |
| β-strand | 17-23 | 7 | 6 |
| β-strand | 25 | 1 | 5 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 7 |
| β-strand | 45-51 | 7 | 7 |
| β-strand | 58-59 | 2 | 7 |
| β-strand | 68-73 | 6 | 6 |
| β-strand | 78-84 | 7 | 6 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 7 |
| β-strand | 107-110 | 4 | 7 |
| β-strand | 114-116 | 3 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-5 | 2 | 8 |
| β-strand | 18-24 | 7 | 8 |
| β-strand | 34-39 | 6 | 9 |
| β-strand | 46-49 | 4 | 9 |
| β-strand | 50 | 1 | 10 |
| β-strand | 54 | 1 | 10 |
| α-helix | 55-56 | 2 | |
| β-strand | 64-68 | 5 | 8 |
| β-strand | 73-78 | 6 | 8 |
| α-helix | 83-85 | 3 | |
| β-strand | 88-93 | 6 | 9 |
| β-strand | 94-95 | 2 | 11 |
| β-strand | 98-99 | 2 | 11 |
| β-strand | 105-106 | 2 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Spike glycoprotein,Fibritin,Expression Tag | C | protein | 1278 | Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T6, synthetic construct | A0A346FJN8, P0DTC2 (AlphaFold model) |
| Heavy chain of R1-26 Fab | H | protein | 139 | Homo sapiens | |
| Light chain of R1-26 Fab | L | protein | 126 | Homo sapiens |
>8ZHG_1 Spike glycoprotein,Fibritin,Expression Tag (chains C) VSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHV SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKV CEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR EFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEK GIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYN SASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFT GCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYF PLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAV LYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGI CASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVS MTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYK TPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIG VTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNF GAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMS ECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFP REGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGS GYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGG SGGGGSGGSAWSHPQFEK
>8ZHG_2 Heavy chain of R1-26 Fab (chains H) MGWSLILLFLVAVATRVLSEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAP GKGLEWVANIKQDGSEKYYVDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARGQL GPWVGVDYWGQGTLVTVSS
>8ZHG_3 Light chain of R1-26 Fab (chains L) MGWSCIILFLVATATGVNFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGS APTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNWVFGG GTQLTV
Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Yan, Q., Gao, X., Liu, B. et al. Nat Commun (2024) 15:7585-7585. DOI 10.1038/s41467-024-51770-3 · PubMed
Other PDB entries of the same protein (UniProt A0A346FJN8), best resolution first:
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