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- EMDB-56135: CD163 bound to haemoglobin -

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Basic information

Entry
Database: EMDB / ID: EMD-56135
TitleCD163 bound to haemoglobin
Map dataSharpened composite map
Sample
  • Complex: CD163 trimer bound to haemoglobin
    • Protein or peptide: Scavenger receptor cysteine-rich type 1 protein M130
    • Protein or peptide: Hemopressin
    • Protein or peptide: Spinorphin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: OXYGEN MOLECULE
KeywordsCD163 / haemoglobin / haptoglobin-haemoglobin receptor / CELL ADHESION
Function / homology
Function and homology information


scavenger receptor activity / CD163 mediating an anti-inflammatory response / cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex ...scavenger receptor activity / CD163 mediating an anti-inflammatory response / cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / erythrocyte development / endocytic vesicle lumen / blood vessel diameter maintenance / acute-phase response / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / Late endosomal microautophagy / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / endocytic vesicle membrane / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / scaffold protein binding / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / external side of plasma membrane / heme binding / Neutrophil degranulation / : / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : ...SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit beta / Hemoglobin subunit alpha / Scavenger receptor cysteine-rich type 1 protein M130
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhou RX / Higgins MK
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust218482/Z/19/Z United Kingdom
CitationJournal: PLoS Biol / Year: 2026
Title: Structural basis for hemoglobin scavenging by CD163 reveals mechanism of ligand promiscuity.
Authors: Richard X Zhou / Matthew K Higgins /
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 ...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.
History
DepositionDec 20, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56135.png

Downloads & links

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Map

FileDownload / File: emd_56135.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.001687344 - 2.2064266
Average (Standard dev.)0.00061572716 (±0.01757422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened composite map

Fileemd_56135_additional_1.map
AnnotationUnsharpened composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CD163 trimer bound to haemoglobin

EntireName: CD163 trimer bound to haemoglobin
Components
  • Complex: CD163 trimer bound to haemoglobin
    • Protein or peptide: Scavenger receptor cysteine-rich type 1 protein M130
    • Protein or peptide: Hemopressin
    • Protein or peptide: Spinorphin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: OXYGEN MOLECULE

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Supramolecule #1: CD163 trimer bound to haemoglobin

SupramoleculeName: CD163 trimer bound to haemoglobin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Scavenger receptor cysteine-rich type 1 protein M130

MacromoleculeName: Scavenger receptor cysteine-rich type 1 protein M130 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.594805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKLRMVLLE DSGSADFRRH FVNLSPFTIT VVLLLSACFV TSSLGGTDKE LRLVDGENKC SGRVEVKVQE EWGTVCNNGW SMEAVSVIC NQLGCPTAIK APGWANSSAG SGRIWMDHVS CRGNESALWD CKHDGWGKHS NCTHQQDAGV TCSDGSNLEM R LTRGGNMC ...String:
MSKLRMVLLE DSGSADFRRH FVNLSPFTIT VVLLLSACFV TSSLGGTDKE LRLVDGENKC SGRVEVKVQE EWGTVCNNGW SMEAVSVIC NQLGCPTAIK APGWANSSAG SGRIWMDHVS CRGNESALWD CKHDGWGKHS NCTHQQDAGV TCSDGSNLEM R LTRGGNMC SGRIEIKFQG RWGTVCDDNF NIDHASVICR QLECGSAVSF SGSSNFGEGS GPIWFDDLIC NGNESALWNC KH QGWGKHN CDHAEDAGVI CSKGADLSLR LVDGVTECSG RLEVRFQGEW GTICDDGWDS YDAAVACKQL GCPTAVTAIG RVN ASKGFG HIWLDSVSCQ GHEPAIWQCK HHEWGKHYCN HNEDAGVTCS DGSDLELRLR GGGSRCAGTV EVEIQRLLGK VCDR GWGLK EADVVCRQLG CGSALKTSYQ VYSKIQATNT WLFLSSCNGN ETSLWDCKNW QWGGLTCDHY EEAKITCSAH REPRL VGGD IPCSGRVEVK HGDTWGSICD SDFSLEAASV LCRELQCGTV VSILGGAHFG EGNGQIWAEE FQCEGHESHL SLCPVA PRP EGTCSHSRDV GVVCSRYTEI RLVNGKTPCE GRVELKTLGA WGSLCNSHWD IEDAHVLCQQ LKCGVALSTP GGARFGK GN GQIWRHMFHC TGTEQHMGDC PVTALGASLC PSEQVASVIC SGNQSQTLSS CNSSSLGPTR PTIPEESAVA CIESGQLR L VNGGGRCAGR VEIYHEGSWG TICDDSWDLS DAHVVCRQLG CGEAINATGS AHFGEGTGPI WLDEMKCNGK ESRIWQCHS HGWGQQNCRH KEDAGVICSE FMSLRLTSEA SREACAGRLE VFYNGAWGTV GKSSMSETTV GVVCRQLGCA DKGKINPASL DKAMSIPMW VDNVQCPKGP DTLWQCPSSP WEKRLASPSE ETWITCDNKI RLQEGPTSCS GRVEIWHGGS WGTVCDDSWD L DDAQVVCQ QLGCGPALKA FKEAEFGQGT GPIWLNEVKC KGNESSLWDC PARRWGHSEC GHKEDAAVNC TDISVQKTPQ KA TTGRSSR QSSFIAVGIL GVVLLAIFVA LFFLTKKRRQ RQRLAVSSRG ENLVHQIQYR EMNSCLNADD LDLMNSSENS HES ADFSAA ELISVSKFLP ISGMEKEAIL SHTEKENGNL

UniProtKB: Scavenger receptor cysteine-rich type 1 protein M130

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Macromolecule #2: Hemopressin

MacromoleculeName: Hemopressin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.28155 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHA HKLRVDPVNF KLLSHCLLVT LAAHLPAEFT PAVHASLDKF LASVSTVLTS KYR

UniProtKB: Hemoglobin subunit alpha

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Macromolecule #3: Spinorphin

MacromoleculeName: Spinorphin / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.021396 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATL SELHCDKLHV DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA NALAHKYH

UniProtKB: Hemoglobin subunit beta

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 16 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 7 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #8: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 8 / Number of copies: 4 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1033649
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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