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- EMDB-52082: Unliganded trimeric CD163 with disordered arms -

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Basic information

Entry
Database: EMDB / ID: EMD-52082
TitleUnliganded trimeric CD163 with disordered arms
Map dataDeep EMhancer sharpened map
Sample
  • Complex: CD163
    • Other: CD163
KeywordsCD163 / haptoglobin-haemoglobin complex / haemoglobin detoxification / ligand uptake / scavenger receptor / SRCR domain-containing protein / ENDOCYTOSIS
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsZhou RX / Higgins MK
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust218482/Z/19/Z United Kingdom
Wellcome Trust220797/Z/20/Z United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Scavenger receptor CD163 multimerises to allow uptake of diverse ligands.
Authors: Richard X Zhou / Matthew K Higgins /
Abstract: CD163 is an archetypal scavenger receptor and mediates detoxification of free haemoglobin. Release of haemoglobin from lysed erythrocytes causes oxidative tissue and organ damage. Detoxification ...CD163 is an archetypal scavenger receptor and mediates detoxification of free haemoglobin. Release of haemoglobin from lysed erythrocytes causes oxidative tissue and organ damage. Detoxification involves haemoglobin binding to the abundant serum protein haptoglobin, followed by CD163-mediated uptake of stoichiometrically diverse haptoglobin-haemoglobin complexes into macrophages for degradation. We show that CD163 adopts dimeric and trimeric assemblies due to calcium-mediated interactions within a membrane-associated base. Arms protrude from this base and create a ligand-binding site. Flexibility within the base, coupled with multiple small ligand-binding surfaces on each arm, allow the receptor to mould around its ligands, resulting in promiscuous uptake of ligands with different structures and stoichiometries. Monomeric CD163 lacks this ability to internalise lower-avidity ligands. Arms from adjacent protomers can also self-associate, blocking ligand-binding surfaces in an autoinhibited state. Therefore, through calcium-dependent multimer formation and flexible ligand binding, CD163 scavenges ligands with different structures and avidities, mediating haemoglobin detoxification.
History
DepositionNov 14, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52082.png

Downloads & links

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Map

FileDownload / File: emd_52082.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeep EMhancer sharpened 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: 0.05
Minimum - Maximum-0.0017761802 - 2.2145228
Average (Standard dev.)0.00038015324 (±0.0126835685)
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 map

Fileemd_52082_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_52082_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_52082_half_map_2.map
Annotationhalf map A
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

EntireName: CD163
Components
  • Complex: CD163
    • Other: CD163

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Supramolecule #1: CD163

SupramoleculeName: CD163 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CD163

MacromoleculeName: CD163 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSKLRMVLLE DSGSADFRRH FVNLSPFTIT VVLLLSACFV TSSLGGTDKE LRLVDGENKC SGRVEVKVQ EEWGTVCNNG WSMEAVSVIC NQLGCPTAIK APGWANSSAG SGRIWMDHVS C RGNESALW DCKHDGWGKH SNCTHQQDAG VTCSDGSNLE MRLTRGGNMC ...String:
MSKLRMVLLE DSGSADFRRH FVNLSPFTIT VVLLLSACFV TSSLGGTDKE LRLVDGENKC SGRVEVKVQ EEWGTVCNNG WSMEAVSVIC NQLGCPTAIK APGWANSSAG SGRIWMDHVS C RGNESALW DCKHDGWGKH SNCTHQQDAG VTCSDGSNLE MRLTRGGNMC SGRIEIKFQG RW GTVCDDN FNIDHASVIC RQLECGSAVS FSGSSNFGEG SGPIWFDDLI CNGNESALWN CKH QGWGKH NCDHAEDAGV ICSKGADLSL RLVDGVTECS GRLEVRFQGE WGTICDDGWD SYDA AVACK QLGCPTAVTA IGRVNASKGF GHIWLDSVSC QGHEPAIWQC KHHEWGKHYC NHNED AGVT CSDGSDLELR LRGGGSRCAG TVEVEIQRLL GKVCDRGWGL KEADVVCRQL GCGSAL KTS YQVYSKIQAT NTWLFLSSCN GNETSLWDCK NWQWGGLTCD HYEEAKITCS AHREPRL VG GDIPCSGRVE VKHGDTWGSI CDSDFSLEAA SVLCRELQCG TVVSILGGAH FGEGNGQI W AEEFQCEGHE SHLSLCPVAP RPEGTCSHSR DVGVVCSRYT EIRLVNGKTP CEGRVELKT LGAWGSLCNS HWDIEDAHVL CQQLKCGVAL STPGGARFGK GNGQIWRHMF HCTGTEQHMG DCPVTALGA SLCPSEQVAS VICSGNQSQT LSSCNSSSLG PTRPTIPEES AVACIESGQL R LVNGGGRC AGRVEIYHEG SWGTICDDSW DLSDAHVVCR QLGCGEAINA TGSAHFGEGT GP IWLDEMK CNGKESRIWQ CHSHGWGQQN CRHKEDAGVI CSEFMSLRLT SEASREACAG RLE VFYNGA WGTVGKSSMS ETTVGVVCRQ LGCADKGKIN PASLDKAMSI PMWVDNVQCP KGPD TLWQC PSSPWEKRLA SPSEETWITC DNKIRLQEGP TSCSGRVEIW HGGSWGTVCD DSWDL DDAQ VVCQQLGCGP ALKAFKEAEF GQGTGPIWLN EVKCKGNESS LWDCPARRWG HSECGH KED AAVNCTDISV QKTPQKATTG RSSRQSSFIA VGILGVVLLA IFVALFFLTK KRRQRQR LA VSSRGENLVH QIQYREMNSC LNADDLDLMN SSENSHESAD FSAAELISVS KFLPISGM E KEAILSHTEK ENGNL
Recombinant expressionOrganism: Homo sapiens (human)

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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: 7.5
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: 42.82 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: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81871
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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