6u53 | pdb_00006u53

Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)

spinqualitylabelsall models 6u53, resolution 1.49Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6u53 is a 1 chain structure with sequence from Lama glama. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.49Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed We had previously shown that three anti-Marburgvirus nanobodies (VHH or sdAb) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution. Here, we wished to determine whether an anti-Ebola virus sdAb, that was cross-reactive within the Ebolavirus genus, recognized a similar structural feature upstream of the ebolaviral NP C-terminus. Additionally, we sought to determine whether the specificities of a less cross-reactive anti-Zaire ebolavirus sdAb and a totally specific anti-Sudan ebolavirus sdAb were the result of exclusion from this region. Binding and X-ray crystallographic studies revealed that the primary determinant of cross-reactivity did indeed appear to be a preference for the helical feature. Specificity, in the case of the Zaire ebolavirus specific sdAb arose from the footprint shifting away from the helices, to engage more variable residues. While both sdAb employed CDRs they also had atypical side-on approaches with framework 2 (FR2) helping to accommodate parts of the epitope in sizeable paratope gullies. The Sudan ebolavirus specific sdAb was more remarkable and appeared to bind two C-terminal domains simultaneously via non-overlapping epitopes - "paratope duality". One mode involved paratope gullying, while the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an inter-domain crevice. The varied routes used by sdAb to engage antigen discovered here deepen our appreciation of the small scaffold's architectural versatility, and also reveal lucrative opportunities within the ebolavirus NP C-termini that might be leveraged for diagnostics and novel therapeutic targeting. Paratope duality and gullying are among the atypical recognition mechanisms employed by a trio of nanobodies to differentiate ebolavirus nucleoproteins.,Sherwood LJ, Taylor AB, Hart PJ, Hayhurst A J Mol Biol. 2019 Oct 15. pii: S0022-2836(19)30597-2. doi:, 10.1016/j.jmb.2019.10.005. PMID:31626803 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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