9TQD | pdb_00009tqd

CD163 bound to haemoglobin

PDB DOI: https://doi.org/10.2210/pdb9TQD/pdb
EM Map EMD-56135: EMDB EMDataResource

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-12-20 Released: 2026-04-15
Deposition Author(s): Zhou, R.X., Higgins, M.K.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for hemoglobin scavenging by CD163 reveals mechanism of ligand promiscuity.

Zhou, R.X., Higgins, M.K.

(2026) PLoS Biol 24: e3003788-e3003788

PubMed: 42133656 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pbio.3003788
Primary Citation Related Structures:
9TQD

PubMed Abstract:
The scavenger receptor CD163 detoxifies free hemoglobin released on erythrocyte lysis to prevent oxidative damage. The best understood route for hemoglobin detoxification involves the formation of haptoglobin-hemoglobin complexes that bind CD163 and are internalized into macrophages, resulting in hemoglobin degradation. However, during conditions such as sickle cell anemia or malaria, haptoglobin is depleted. CD163 can then act as a lower-affinity receptor for free hemoglobin. Previous studies revealed that CD163 forms a multimeric "base," which presents "arms" that form a binding site for haptoglobin-hemoglobin. In this study, we use cryogenic electron microscopy to reveal how human CD163 binds hemoglobin tetramers in a process that, unlike haptoglobin-hemoglobin uptake, requires a full trimeric CD163 assembly to achieve sufficient binding. We reveal how flexibility at the calcium-mediated base, combined with a hinge between receptor domains 2 and 3, allows the arms to wrap around diverse ligands. This brings together multiple small binding surfaces from different domains to form cradles for different ligands. These adaptations allow the scavenger receptor to be promiscuous, protecting us from oxidative damage caused by hemoglobin release in various pathological conditions.

Organizational Affiliation

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 446.52 kDa
Atom Count: 24,023
Modeled Residue Count: 3,110
Deposited Residue Count: 4,046
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor cysteine-rich type 1 protein M130	A, B, C	1,156	Homo sapiens	Mutation(s): 0 Gene Names: CD163, M130
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VB7 (Homo sapiens) Explore Q86VB7 Go to UniProtKB: Q86VB7
PHAROS: Q86VB7 GTEx: ENSG00000177575
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86VB7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: Q86VB7-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemopressin	D, F	142	Homo sapiens	Mutation(s): 0 Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905 Go to UniProtKB: P69905
PHAROS: P69905 GTEx: ENSG00000188536 ENSG00000206172
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spinorphin	E, G	147	Homo sapiens	Mutation(s): 0 Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871 Go to UniProtKB: P68871
PHAROS: P68871 GTEx: ENSG00000244734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, J, K, L	2		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain KA [auth D] SDF format, chain MA [auth E] SDF format, chain OA [auth F] SDF format, chain QA [auth G] MOL2 format, chain KA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain QA [auth G] mmCIF format, chain KA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain QA [auth G]	KA [auth D], MA [auth E], OA [auth F], QA [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain KA [auth D] Focus chain MA [auth E] Focus chain OA [auth F] Focus chain QA [auth G] Interactions & Density Focus chain KA [auth D] Focus chain MA [auth E] Focus chain OA [auth F] Focus chain QA [auth G]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B]	EA [auth C] M [auth A] N [auth A] O [auth A] P [auth A] EA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], W [auth B], X [auth B], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain Z [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] FA [auth C] AA [auth B], BA [auth B], CA [auth B], DA [auth B], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain NA [auth E] SDF format, chain PA [auth F] SDF format, chain RA [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain RA [auth G] mmCIF format, chain LA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain PA [auth F] mmCIF format, chain RA [auth G]	LA [auth D], NA [auth E], PA [auth F], RA [auth G]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Focus chain NA [auth E] Focus chain PA [auth F] Focus chain RA [auth G] Interactions & Density Focus chain LA [auth D] Focus chain NA [auth E] Focus chain PA [auth F] Focus chain RA [auth G]