7XQV image
Deposition Date 2022-05-09
Release Date 2022-07-13
Last Version Date 2024-10-30
Entry Detail
PDB ID:
7XQV
Keywords:
Title:
The complex of nanobody Rh57 binding to GTP-bound RhoA active form
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.76 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
I 41 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:RhoA
Chain IDs:A
Chain Length:183
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:Rh57
Chain IDs:B
Chain Length:145
Number of Molecules:1
Biological Source:Camelus bactrianus
Primary Citation
Structural insights into the binding of nanobody Rh57 to active RhoA-GTP.
Biochem.Biophys.Res.Commun. 616 122 128 (2022)
PMID: 35665664 DOI: 10.1016/j.bbrc.2022.05.084

Abstact

RhoA protein is a small GTPase that acts as a molecular switch. When bound to guanosine triphosphate (GTP), RhoA can activate several key signal pathways. Recently, nanobody Rh57 specific binding with GTP bound active RhoA was discovered and developed as a BRET biosensor without cytotoxicity. To further clarify the nanobody Rh57's mechanism of action, we co-expressed, purified, and crystallized the RhoA-Rh57 nanobody complex and solved the structure by X-ray diffraction with a resolution of 2.76 Å. The structure showed that the interaction is mainly through hydrogen bonds, salt bridges, aromatic-aromatic interactions, and hydrophobic interactions. The involved regions include CDR3 and non-hypervariable loop of Rh57, and the SWI switch loops of RhoA, respectively. The different SWI conformation of inactivated RhoA-GDP prevented the Rh57's binding. The possible explanation of Rh57 as a non-cytotoxic BRET intracellular tracer is that Rh57's binding did not overlap with downstream PRK1 and thus did not interfere with the downstream signaling pathway. Our research provides an in-depth understanding of how nanobodies recognize activated RhoA-GTP while not binding inactivated RhoA-GDP. This structural information may also provide critical information for further optimization of relevant nanobodies.

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