9NB5 image
Deposition Date 2025-02-13
Release Date 2025-06-18
Last Version Date 2025-07-23
Entry Detail
PDB ID:
9NB5
Keywords:
Title:
Cryo-EM structure of the autoinhibitory CD163 trimer
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
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:A, B, C
Chain Length:1012
Number of Molecules:3
Biological Source:Homo sapiens
Primary Citation
Structural elucidation of the haptoglobin-hemoglobin clearance mechanism by macrophage scavenger receptor CD163.
Plos Biol. 23 e3003264 e3003264 (2025)
PMID: 40644526 DOI: 10.1371/journal.pbio.3003264

Abstact

Intravascular hemolysis releases hemoglobin into the bloodstream, which can damage vascular and renal tissues due to its oxidative nature. Circulating haptoglobin acts as a primary defense by binding to free hemoglobin, forming a haptoglobin-hemoglobin (HpHb) complex that is then recognized and cleared by the CD163 scavenger receptor on macrophages. While the function and structure of HpHb complex are mostly well-defined, the molecular mechanism underlying its interaction with CD163 remains unclear. Here we report the cryo-electron microscopy structures of human CD163 in its unliganded state and in its complex with HpHb. These structures reveal that CD163 functions as a trimer, forming a composite binding site at its center for one protomer of the dimeric HpHb, resulting in a 3:1 binding stoichiometry. In the unliganded state, CD163 can also form a trimer, but in an autoinhibitory configuration that occludes the ligand binding site. Widespread electrostatic interactions mediated by calcium ions are pivotal in both pre-ligand and ligand-bound receptor assemblies. This calcium-dependent mechanism enables CD163/HpHb complexes to assemble and, once internalized, disassemble into individual components upon reaching the endosome, where low calcium and lower pH conditions prevail. Collectively, this study elucidates the molecular mechanism by which CD163-mediated endocytosis efficiently clears different isoforms of HpHb.

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