7ZSD: Omicron spike

cryo-EM structure of omicron spike in complex with de novo designed binder, local. Determined by electron microscopy at 3.29 Å resolution. Released 1 Mar 2023.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Drosophila melanogaster
Chains: 2
Atoms: 2,120
Mol. weight: 31.53 kDa
Released: 1 Mar 2023

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

Secondary structure: helices and β-sheets

7ZSD contains 16 α-helices and 10 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 M: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	1
α-helix	336	1
α-helix	338-342	5
α-helix	347-349	3
α-helix	350-352	3
β-strand	354-358	5	2
β-strand	362	1	1
α-helix	366-370	5
β-strand	376	1	2
β-strand	379-380	2	2
α-helix	384-389	6
β-strand	395-403	9	2
α-helix	404-409	6
α-helix	417	1
α-helix	418-422	5
β-strand	431-437	7	2
β-strand	452-454	3	3
α-helix	460-462	3
α-helix	471-473	3
β-strand	492-494	3	3
β-strand	507-514	8	2

Chain P: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-23	20
α-helix	27-48	22
α-helix	51-54	4
α-helix	59-61	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	M	protein	196	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
de novo designed binder	P	protein	79	Drosophila melanogaster	Q9VKJ9 (AlphaFold model)

Sequence of entity 1 (M), FASTA

>7ZSD_1 Spike glycoprotein (chains M)
ITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLC
FTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNY
LYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVV
VLSFELLHAPATVCGP

Sequence of entity 2 (P), FASTA

>7ZSD_2 de novo designed binder (chains P)
ETGASSTNMLEALQQRLQFYHGQVARAALENNSGKARRFGRIVKQYEDAIKLYKAGKPVP
YDELPVPPGFGGSENLYFQ

Primary citation

De novo design of protein interactions with learned surface fingerprints. Gainza, P., Wehrle, S., Van Hall-Beauvais, A. et al. Nature (2023) 617:176-184. DOI 10.1038/s41586-023-05993-x · PubMed

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

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
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…

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