7B3Y: Nanoparticle for a COVID-19 vaccine candidate

Structure of a nanoparticle for a COVID-19 vaccine candidate. Determined by electron microscopy at 3.7 Å resolution. Released 13 Jan 2021.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Streptococcus pyogenes serotype M49 (strain NZ131), Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Chains: 1
Atoms: 1,516
Mol. weight: 36 kDa
Released: 13 Jan 2021

Explore 7B3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B3Y contains 12 α-helices and 10 β-strands across 1 chain. 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 B: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
β-strand	10-14	5	1
α-helix	19-31	13
β-strand	36-40	5	1
α-helix	46-53	8
α-helix	54-59	6
β-strand	62-66	5	1
α-helix	71-79	9
β-strand	84-86	3	1
α-helix	92-101	10
β-strand	104-106	3	1
β-strand	108-109	2	2
α-helix	112-120	9
β-strand	125-128	4	2
α-helix	131-134	4
α-helix	136-143	8
β-strand	150-153	4	2
β-strand	154	1	1
α-helix	162-168	7
β-strand	173-175	3	1
α-helix	177-180	4
α-helix	184-199	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate…	B	protein	341	Streptococcus pyogenes serotype M49 (strain NZ131), Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)	A0A0H3BX48 (AlphaFold model), Q9WXS1 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7B3Y_1 Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (chains B)
MGSSVTTLSGLSGEQGPSGDMTTEEDSATHIKFSKRDEDGRELAGATMELRDSSGKTIST
WISDGHVKDFYLYPGKYTFVETAAPDGYEVATPIEFTVNEDGQVTVDGEATEGDAHTGGS
GGSGGSGGSMKMEELFKKHKIVAVLRANSVEEAKKKALAVFLGGVHLIEITFTVPDADTV
IKELSFLKEMGAIIGAGTVTSVEQARKAVESGAEFIVSPHLDEEISQFAKEKGVFYMPGV
MTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAG
VLAVGVGSALVKGTPVEVAEKAKAFVEKIRGCTEGSGEPEA

Primary citation

A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses. Tan, T.K., Rijal, P., Rahikainen, R. et al. Nat Commun (2021) 12:542-542. DOI 10.1038/s41467-020-20654-7 · PubMed

Browse structure collections

About this viewer

MolViewer shows 7B3Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.