8XMW image
Deposition Date 2023-12-28
Release Date 2025-01-01
Last Version Date 2025-08-06
Entry Detail
PDB ID:
8XMW
Keywords:
Title:
Local refinement of Hb-Hp bind to CD163
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.94 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Isoform 2 of Haptoglobin
Gene (Uniprot):HP
Chain IDs:A (auth: 2)
Chain Length:347
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hemoglobin subunit alpha
Gene (Uniprot):HBA1, HBA2
Chain IDs:D (auth: A)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hemoglobin subunit beta
Gene (Uniprot):HBB
Chain IDs:E (auth: B)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Scavenger receptor cysteine-rich type 1 protein M130
Gene (Uniprot):CD163
Chain IDs:B (auth: D), C (auth: G)
Chain Length:1009
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Calcium-dependent oligomerization of scavenger receptor CD163 facilitates the endocytosis of ligands.
Nat Commun 16 6679 6679 (2025)
PMID: 40691148 DOI: 10.1038/s41467-025-62013-4

Abstact

Scavenger receptor CD163 is a marker of M2 type macrophages that play important roles in anti-inflammatory processes. The most extensively studied function of CD163 is related to the elimination of hemoglobin-haptoglobin (Hb-Hp) complexes, to prevent potential oxidative toxicity of the iron-containing heme. However, the structural mechanism of CD163 in ligand binding and internalization remains elusive. Here, we present the cryo-electron microscopy structure of human Hb-Hp recognition by the full ectodomain of CD163. We illuminate that CD163 forms calcium-dependent oligomers and primarily exists as trimeric form under the condition of 2.5 mM calcium. It mainly utilizes two protomers to interact with Hb-Hp complex asymmetrically, while the third protomer of the trimer also has the potential to form calcium-mediated contacts with Hp. Flow cytometry analyses reveal that oligomerization of CD163 significantly enhances the efficiency of ligand endocytosis. These results advance our understanding of the role of CD163 in ligand scavenging.

Legend

Protein

Chemical

Disease

Primary Citation of related structures