8E01: Engineered nano-cage fusion protein

Structure of engineered nano-cage fusion protein. Determined by electron microscopy at 3.4 Å resolution. Released 16 Nov 2022.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Thermotoga maritima
Chains: 1
Atoms: 1,518
Mol. weight: 23.92 kDa
Released: 16 Nov 2022

Explore 8E01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E01 contains 10 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 A: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	25-29	5
β-strand	31-35	5	1
α-helix	40-52	13
β-strand	57-61	5	1
α-helix	67-73	7
α-helix	76-79	4
β-strand	83-87	5	1
α-helix	92-100	9
β-strand	105-107	3	2
α-helix	113-122	10
β-strand	125-127	3	2
β-strand	129-130	2	3
α-helix	133-142	10
β-strand	146-149	4	3
α-helix	157-163	7
β-strand	171-173	3	3
β-strand	175	1	1
α-helix	183-189	7
β-strand	194-196	3	1
α-helix	205-221	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase	A	protein	224	Thermotoga maritima	Q9WXS1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8E01_1 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (chains A)
MHHHHHHGGSGGSGGSGGSMKMEELFKKHKIVAVLRANSVEEAKKKALAVFLGGVHLIEI
TFTVPDADTVIKELSFLKEMGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCK
EKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNL
DNVCEWFKAGVLAVGVGSALVKGTPVEVAEKAKAFVEKIRGCTE

Primary citation

Intranasal SARS-CoV-2 RBD decorated nanoparticle vaccine enhances viral clearance in the Syrian hamster model. Patel, D.R., Minns, A.M., Sims, D.G. et al. bioRxiv (2022). DOI 10.1101/2022.10.27.514054 · PubMed

Other PDB entries of the same protein (UniProt Q9WXS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WA3 1.9 Å, Mechanism of the Class I KDPG aldolase
9UAQ 2.29 Å, CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
1VLW 2.3 Å, Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate…
9UCL 2.43 Å, CryoEM structure of IgV domain of human Nectin-4 with Trimbody
9XOU 2.5 Å, CryoEM structure of LacY with Trimbody
9UBR 2.62 Å, CryoEM structure of human Galectin-10 with iTrimbody
8SZZ 2.9 Å, CryoEM Structure of Computationally Designed Nanocage O32-ZL4
8TVB 2.9 Å, Ghanaian virus fusion glycoprotein (GhV F)
8TYC 3.3 Å, Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1
8JGC 3.44 Å, Cryo-EM structure of Mi3 fused with LOV2
8JGA 3.68 Å, Cryo-EM structure of Mi3 fused with FKBP
7B3Y 3.7 Å, Structure of a nanoparticle for a COVID-19 vaccine candidate

Browse structure collections

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