7Z8O: SARS-CoV-2 S RBD

Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide. Determined by X-ray diffraction at 0.96 Å resolution. Released 28 Jun 2023.

Method: X-ray diffraction
Resolution: 0.96 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, synthetic construct
Chains: 2
Atoms: 2,136
Mol. weight: 23.97 kDa
Ligands: KZ0
Released: 28 Jun 2023

Explore 7Z8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z8O contains 11 α-helices and 17 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.

Chain A: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	1
α-helix	338-342	5
β-strand	349	1	2
α-helix	350-352	3
β-strand	354-358	5	2
β-strand	361-362	2	1
α-helix	365-369	5
β-strand	376-380	5	2
α-helix	384-389	6
β-strand	391-392	2	1
β-strand	394-403	10	2
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	2
α-helix	439-442	4
β-strand	448	1	3
β-strand	452-454	3	4
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	5
β-strand	485	1	5
β-strand	488-489	2	5
β-strand	492-494	3	4
β-strand	497	1	3
α-helix	503-505	3
β-strand	507-516	10	2
β-strand	524-525	2	1

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	274-276	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	198	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Stapled peptide	B	protein	14	synthetic construct

Sequence of entity 1 (A), FASTA

>7Z8O_1 Spike protein S1 (chains A)
GSGTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLND
LCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNY
NYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYR
VVVLSFELLHAPATVCGP

Sequence of entity 2 (B), FASTA

>7Z8O_2 Stapled peptide (chains B)
XCPYVAGXATCLXC

Ligands and cofactors

ID	Name	Formula	Copies
KZ0	2,4,6-tris(chloromethyl)-1,3,5-triazine	C6 H6 Cl3 N3	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2. Gaynor, K.U., Vaysburd, M., Harman, M.A.J. et al. Nat Commun (2023) 14:3583-3583. DOI 10.1038/s41467-023-39158-1 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

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