Journal:IUCrJ:S2052252521005340

X-ray crystallography studies of RoAb13 bound to PIYDIN, a part of the CCR5 N-terminal domain

Lata Govada, Emmanuel Saridakis, Sean C. Kassen, Ahmad Bin-Ramzi, Rhodri Marc Morgan, Benjamin Chain, John R. Helliwell and Naomi E. Chayen ^[1]

Molecular Tour
Although it is to an extent held in check in the industrialized world thanks to antiviral drugs, AIDS is still endemic in many parts of the world, claiming nearly 700,000 lives annually. It is thought that anti-HIV vaccination, when available, will be more efficient against the disease in the long term, especially where regular, well-organized healthcare is lacking. However, HIV mutates rapidly, and stimulating a response which protects against all variants remains challenging. An alternative is to target a host protein which is essential for the virus to enter cells and produce AIDS.

targets a short N-terminal region of the protein CCR5, which is the main entry receptor of HIV into the human organism. Blocking that receptor would therefore prevent HIV infection and replication. We had earlier reported the structure of the antibody alone by X-ray crystallography (Chain et al. 2015^[2]), but the structure of the antibody complexed to the part of CCR5 to which it binds (its epitope) had remained elusive. That structure is important for designing efficient vaccines based on short synthetic immunogenic peptides that mimic the CCR5 antibody-binding region.

Figure 1a Crystals of RoAb13 complexed with the 31 peptide. X-ray crystallography.

Figure 1b Crystals of RoAb13 complexed with the PIYDIN peptide

After a long search for co-crystallization conditions involving both the whole N-terminal region of CCR5 and the minimally required binding region to its antibody (the ‘core peptide’), and the analysis and comparison of X-ray crystallographic electron density maps obtained from several crystals, we have finally located the core peptide of the CCR5 receptor bound to RoAb13. It binds at the hypervariable region ‘CDR3’ of the antibody’s light chain, an expected antigen-binding site. In spite of the fact that the best attainable resolution is not particularly high at 3 Å, we have been able to identify (both cases).

; PIYDIN is colored in orange, antibody RoAb13 in cyan/green. We observe that, in the case of the PIYDIN part of the 31 peptide, of the ligand is near (approximately within 3.5 Å of) tyrosines 98 and 100, and of the Light chain. of the Heavy chain. is only engaged in intra-peptide interactions, with Ile12 and Asn13.

In the , Ile9 (in hot pink) additionally comes near (in deep sky blue) of the Light chain. The corresponding distance is ca. 5 Å for the 31 peptide structure (Ile9 is in orange; Thr99 in cyan). PIYDIN is colored in magenta, antibody RoAb13 in cyan/green.

The PIYDIN of the 31 peptide study (Figure 2a):

• .
• .

The PIYDIN only study (Figure 2b):

• .
• .

The overlay of both with the 31 peptide; the peptide is not in exactly the same placement but very similar (Figure 2c):

• . The PIYDIN of the 31 peptide study is in orange, the PIYDIN only study is in magenta.
• .

• , both peptides are in magenta, antibody RoAb13 is in cyan/green.

Furthermore, the core peptide was found to bind in a way that can accommodate the full length of the CCR5 N-terminus.

The structural insights thus may inform the design of better peptide analogues for use as immunogens in vivo. These analogues may ultimately provide the basis for active immunization vaccines to stimulate an antibody response to native CCR5 which will thwart HIV infection.

PDB references: RoAb13, bound to 31-residue peptide containing the PIYDIN sequence, 7njz; bound to PIYDIN peptide, 7nw3.

References

1. ↑ Govada L, Saridakis E, Kassen SC, Bin-Ramzi A, Morgan RM, Chain B, Helliwell JR, Chayen NE. X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5. IUCrJ. 2021 Jul 1;8(Pt 4):678-683. doi: 10.1107/S2052252521005340. eCollection, 2021 Jul 1. PMID:34258015 doi:http://dx.doi.org/10.1107/S2052252521005340
2. ↑ Chain B, Arnold J, Akthar S, Brandt M, Davis D, Noursadeghi M, Lapp T, Ji C, Sankuratri S, Zhang Y, Govada L, Saridakis E, Chayen N. A Linear Epitope in the N-Terminal Domain of CCR5 and Its Interaction with Antibody. PLoS One. 2015 Jun 1;10(6):e0128381. doi: 10.1371/journal.pone.0128381., eCollection 2015. PMID:26030924 doi:http://dx.doi.org/10.1371/journal.pone.0128381