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- EMDB-52080: Unliganded dimeric CD163 with arm-arm contacts -

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Basic information

Entry
Database: EMDB / ID: EMD-52080
TitleUnliganded dimeric CD163 with arm-arm contacts
Map dataDeep EMhancer sharpened map
Sample
  • Complex: CD163
    • Protein or peptide: Scavenger receptor cysteine-rich type 1 protein M130
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsCD163 / haptoglobin-haemoglobin complex / haemoglobin detoxification / ligand uptake / scavenger receptor / SRCR domain-containing protein / ENDOCYTOSIS
Function / homology
Function and homology information


CD163 mediating an anti-inflammatory response / scavenger receptor activity / Scavenging of heme from plasma / acute-phase response / endocytic vesicle membrane / scaffold protein binding / external side of plasma membrane / extracellular region / 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
Similarity search - Domain/homology
Scavenger receptor cysteine-rich type 1 protein M130
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: To Be Published
Title: Scavenger receptor CD163 multimerises to allow uptake of diverse ligands
Authors: Zhou RX / Higgins MK
History
DepositionNov 14, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52080.png

Downloads & links

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Map

FileDownload / File: emd_52080.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: 0.07
Minimum - Maximum-0.00174695 - 2.4580464
Average (Standard dev.)0.00038506213 (±0.014410052)
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_52080_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_52080_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_52080_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
    • Protein or peptide: Scavenger receptor cysteine-rich type 1 protein M130
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: CD163

SupramoleculeName: CD163 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 2 / 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 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 723620
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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