6C1Q image
Deposition Date 2018-01-05
Release Date 2018-05-30
Last Version Date 2025-04-02
Entry Detail
PDB ID:
6C1Q
Title:
Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.28
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
Gene (Uniprot):cybC, C5AR1
Mutagens:M29W, H124I, R128L
Chain IDs:A (auth: B)
Chain Length:422
Number of Molecules:1
Biological Source:Escherichia coli, Homo sapiens
Polymer Type:polypeptide(L)
Molecule:PMX53
Chain IDs:B (auth: L)
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
YCM A CYS modified residue
Ligand Molecules
Peptide-like Molecules
PRD_002303
Primary Citation
Orthosteric and allosteric action of the C5a receptor antagonists.
Nat. Struct. Mol. Biol. 25 472 481 (2018)
PMID: 29867214 DOI: 10.1038/s41594-018-0067-z

Abstact

The C5a receptor (C5aR) is a G-protein-coupled receptor (GPCR) that can induce strong inflammatory response to the anaphylatoxin C5a. Targeting C5aR has emerged as a novel anti-inflammatory therapeutic method. However, developing potent C5aR antagonists as drugs has proven difficult. Here, we report two crystal structures of human C5aR in ternary complexes with the peptide antagonist PMX53 and a non-peptide antagonist, either avacopan or NDT9513727. The structures, together with other biophysical, computational docking and cell-based signaling data, reveal the orthosteric action of PMX53 and its effect of stabilizing the C5aR structure, as well as the allosteric action of chemically diverse non-peptide C5aR antagonists with different binding poses. Structural comparison analysis suggests the presence of similar allosteric sites in other GPCRs. We also discuss critical structural features of C5aR in activation, including a novel conformation of helix 8. On the basis of our results, we suggest novel strategies for developing C5aR-targeting drugs.

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Primary Citation of related structures