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- EMDB-49214: Consensus map of the CD163/Hp(1-1)Hb complex (Map G) -

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Basic information

Entry
Database: EMDB / ID: EMD-49214
TitleConsensus map of the CD163/Hp(1-1)Hb complex (Map G)
Map data
Sample
  • Complex: CD163/Hp(1-1)Hb complex
    • Protein or peptide: CD163
    • Protein or peptide: CD163
    • Protein or peptide: CD163
    • Protein or peptide: HBA1
    • Protein or peptide: HBB
    • Protein or peptide: HP
    • Protein or peptide: HBA1
    • Protein or peptide: HBB
    • Protein or peptide: HP
KeywordsCD163 / M130 / Scavenger receptor / Haptoglobin / Hemoglobin / Hb / Hp / Hp(1-1)Hb / HpHb / hemolysis / ENDOCYTOSIS
Function / homology
Function and homology information


negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / zymogen activation / CD163 mediating an anti-inflammatory response / scavenger receptor activity / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption ...negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / zymogen activation / CD163 mediating an anti-inflammatory response / scavenger receptor activity / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / antioxidant activity / oxygen transport / immune system process / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / acute-phase response / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / defense response / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / platelet aggregation / specific granule lumen / 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 / defense response to bacterium / iron ion binding / external side of plasma membrane / serine-type endopeptidase activity / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / 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 / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi ...SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Haptoglobin / 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: 3.3 Å
AuthorsHuang C-S / White JBR / Degtjarik O
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust108466/Z/15/Z United Kingdom
Wellcome Trust221524/Z/20/Z United Kingdom
CitationJournal: To Be Published
Title: Structural elucidation of the haptoglobin-hemoglobin clearance mechanism by macrophage scavenger receptor CD163
Authors: Huang C-S / Wang H / White JBR / Degtjarik O / Huynh C / Brannstrom K / Horn MT / Muench SP / Somers WS / Chaparro-Riggers J / Lin L / Mosyak L
History
DepositionFeb 13, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49214.png

Downloads & links

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Map

FileDownload / File: emd_49214.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 400 pix.
= 444. Å		1.11 Å/pix.
x 400 pix.
= 444. Å		1.11 Å/pix.
x 400 pix.
= 444. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-4.3283515 - 6.1167026
Average (Standard dev.)0.0009534255 (±0.074897796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49214_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49214_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49214_half_map_2.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/Hp(1-1)Hb complex

EntireName: CD163/Hp(1-1)Hb complex
Components
  • Complex: CD163/Hp(1-1)Hb complex
    • Protein or peptide: CD163
    • Protein or peptide: CD163
    • Protein or peptide: CD163
    • Protein or peptide: HBA1
    • Protein or peptide: HBB
    • Protein or peptide: HP
    • Protein or peptide: HBA1
    • Protein or peptide: HBB
    • Protein or peptide: HP

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Supramolecule #1: CD163/Hp(1-1)Hb complex

SupramoleculeName: CD163/Hp(1-1)Hb complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 530 KDa

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Macromolecule #1: CD163

MacromoleculeName: CD163 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSLGGTDKEL RLVDGENKCS GRVEVKVQEE WGTVCNNGWS MEAVSVICNQ LGCPTAIKAP GWANSSAGSG RIWMDHVSCR GNESALWDCK HDGWGKHSNC THQQDAGVTC SDGSNLEMRL TRGGNMCSGR IEIKFQGRWG TVCDDNFNID HASVICRQLE CGSAVSFSGS ...String:
SSLGGTDKEL RLVDGENKCS GRVEVKVQEE WGTVCNNGWS MEAVSVICNQ LGCPTAIKAP GWANSSAGSG RIWMDHVSCR GNESALWDCK HDGWGKHSNC THQQDAGVTC SDGSNLEMRL TRGGNMCSGR IEIKFQGRWG TVCDDNFNID HASVICRQLE CGSAVSFSGS SNFGEGSGPI WFDDLICNGN ESALWNCKHQ GWGKHNCDHA EDAGVICSKG ADLSLRLVDG VTECSGRLEV RFQGEWGTIC DDGWDSYDAA VACKQLGCPT AVTAIGRVNA SKGFGHIWLD SVSCQGHEPA IWQCKHHEWG KHYCNHNEDA GVTCSDGSDL ELRLRGGGSR CAGTVEVEIQ RLLGKVCDRG WGLKEADVVC RQLGCGSALK TSYQVYSKIQ ATNTWLFLSS CNGNETSLWD CKNWQWGGLT CDHYEEAKIT CSAHREPRLV GGDIPCSGRV EVKHGDTWGS ICDSDFSLEA ASVLCRELQC GTVVSILGGA HFGEGNGQIW AEEFQCEGHE SHLSLCPVAP RPEGTCSHSR DVGVVCSRYT EIRLVNGKTP CEGRVELKTL GAWGSLCNSH WDIEDAHVLC QQLKCGVALS TPGGARFGKG NGQIWRHMFH CTGTEQHMGD CPVTALGASL CPSEQVASVI CSGNQSQTLS SCNSSSLGPT RPTIPEESAV ACIESGQLRL VNGGGRCAGR VEIYHEGSWG TICDDSWDLS DAHVVCRQLG CGEAINATGS AHFGEGTGPI WLDEMKCNGK ESRIWQCHSH GWGQQNCRHK EDAGVICSEF MSLRLTSEAS REACAGRLEV FYNGAWGTVG KSSMSETTVG VVCRQLGCAD KGKINPASLD KAMSIPMWVD NVQCPKGPDT LWQCPSSPWE KRLASPSEET WITCDNKIRL QEGPTSCSGR VEIWHGGSWG TVCDDSWDLD DAQVVCQQLG CGPALKAFKE AEFGQGTGPI WLNEVKCKGN ESSLWDCPAR RWGHSECGHK EDAAVNCTDI SVQKTPQKAT TGRSHHHHHH HH

UniProtKB: Scavenger receptor cysteine-rich type 1 protein M130

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Macromolecule #2: CD163

MacromoleculeName: CD163 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSLGGTDKEL RLVDGENKCS GRVEVKVQEE WGTVCNNGWS MEAVSVICNQ LGCPTAIKAP GWANSSAGSG RIWMDHVSCR GNESALWDCK HDGWGKHSNC THQQDAGVTC SDGSNLEMRL TRGGNMCSGR IEIKFQGRWG TVCDDNFNID HASVICRQLE CGSAVSFSGS ...String:
SSLGGTDKEL RLVDGENKCS GRVEVKVQEE WGTVCNNGWS MEAVSVICNQ LGCPTAIKAP GWANSSAGSG RIWMDHVSCR GNESALWDCK HDGWGKHSNC THQQDAGVTC SDGSNLEMRL TRGGNMCSGR IEIKFQGRWG TVCDDNFNID HASVICRQLE CGSAVSFSGS SNFGEGSGPI WFDDLICNGN ESALWNCKHQ GWGKHNCDHA EDAGVICSKG ADLSLRLVDG VTECSGRLEV RFQGEWGTIC DDGWDSYDAA VACKQLGCPT AVTAIGRVNA SKGFGHIWLD SVSCQGHEPA IWQCKHHEWG KHYCNHNEDA GVTCSDGSDL ELRLRGGGSR CAGTVEVEIQ RLLGKVCDRG WGLKEADVVC RQLGCGSALK TSYQVYSKIQ ATNTWLFLSS CNGNETSLWD CKNWQWGGLT CDHYEEAKIT CSAHREPRLV GGDIPCSGRV EVKHGDTWGS ICDSDFSLEA ASVLCRELQC GTVVSILGGA HFGEGNGQIW AEEFQCEGHE SHLSLCPVAP RPEGTCSHSR DVGVVCSRYT EIRLVNGKTP CEGRVELKTL GAWGSLCNSH WDIEDAHVLC QQLKCGVALS TPGGARFGKG NGQIWRHMFH CTGTEQHMGD CPVTALGASL CPSEQVASVI CSGNQSQTLS SCNSSSLGPT RPTIPEESAV ACIESGQLRL VNGGGRCAGR VEIYHEGSWG TICDDSWDLS DAHVVCRQLG CGEAINATGS AHFGEGTGPI WLDEMKCNGK ESRIWQCHSH GWGQQNCRHK EDAGVICSEF MSLRLTSEAS REACAGRLEV FYNGAWGTVG KSSMSETTVG VVCRQLGCAD KGKINPASLD KAMSIPMWVD NVQCPKGPDT LWQCPSSPWE KRLASPSEET WITCDNKIRL QEGPTSCSGR VEIWHGGSWG TVCDDSWDLD DAQVVCQQLG CGPALKAFKE AEFGQGTGPI WLNEVKCKGN ESSLWDCPAR RWGHSECGHK EDAAVNCTDI SVQKTPQKAT TGRSHHHHHH HH

UniProtKB: Scavenger receptor cysteine-rich type 1 protein M130

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Macromolecule #3: CD163

MacromoleculeName: CD163 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSLGGTDKEL RLVDGENKCS GRVEVKVQEE WGTVCNNGWS MEAVSVICNQ LGCPTAIKAP GWANSSAGSG RIWMDHVSCR GNESALWDCK HDGWGKHSNC THQQDAGVTC SDGSNLEMRL TRGGNMCSGR IEIKFQGRWG TVCDDNFNID HASVICRQLE CGSAVSFSGS ...String:
SSLGGTDKEL RLVDGENKCS GRVEVKVQEE WGTVCNNGWS MEAVSVICNQ LGCPTAIKAP GWANSSAGSG RIWMDHVSCR GNESALWDCK HDGWGKHSNC THQQDAGVTC SDGSNLEMRL TRGGNMCSGR IEIKFQGRWG TVCDDNFNID HASVICRQLE CGSAVSFSGS SNFGEGSGPI WFDDLICNGN ESALWNCKHQ GWGKHNCDHA EDAGVICSKG ADLSLRLVDG VTECSGRLEV RFQGEWGTIC DDGWDSYDAA VACKQLGCPT AVTAIGRVNA SKGFGHIWLD SVSCQGHEPA IWQCKHHEWG KHYCNHNEDA GVTCSDGSDL ELRLRGGGSR CAGTVEVEIQ RLLGKVCDRG WGLKEADVVC RQLGCGSALK TSYQVYSKIQ ATNTWLFLSS CNGNETSLWD CKNWQWGGLT CDHYEEAKIT CSAHREPRLV GGDIPCSGRV EVKHGDTWGS ICDSDFSLEA ASVLCRELQC GTVVSILGGA HFGEGNGQIW AEEFQCEGHE SHLSLCPVAP RPEGTCSHSR DVGVVCSRYT EIRLVNGKTP CEGRVELKTL GAWGSLCNSH WDIEDAHVLC QQLKCGVALS TPGGARFGKG NGQIWRHMFH CTGTEQHMGD CPVTALGASL CPSEQVASVI CSGNQSQTLS SCNSSSLGPT RPTIPEESAV ACIESGQLRL VNGGGRCAGR VEIYHEGSWG TICDDSWDLS DAHVVCRQLG CGEAINATGS AHFGEGTGPI WLDEMKCNGK ESRIWQCHSH GWGQQNCRHK EDAGVICSEF MSLRLTSEAS REACAGRLEV FYNGAWGTVG KSSMSETTVG VVCRQLGCAD KGKINPASLD KAMSIPMWVD NVQCPKGPDT LWQCPSSPWE KRLASPSEET WITCDNKIRL QEGPTSCSGR VEIWHGGSWG TVCDDSWDLD DAQVVCQQLG CGPALKAFKE AEFGQGTGPI WLNEVKCKGN ESSLWDCPAR RWGHSECGHK EDAAVNCTDI SVQKTPQKAT TGRSHHHHHH HH

UniProtKB: Scavenger receptor cysteine-rich type 1 protein M130

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Macromolecule #4: HBA1

MacromoleculeName: HBA1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP AVHASLDKFL ASVSTVLTSK YR

UniProtKB: Hemoglobin subunit alpha

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Macromolecule #5: HBB

MacromoleculeName: HBB / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG KEFTPPVQAA YQKVVAGVAN ALAHKYH

UniProtKB: Hemoglobin subunit beta

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Macromolecule #6: HP

MacromoleculeName: HP / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSALGAVIAL LLWGQLFAVD SGNDVTDIAD DGCPKPPEIA HGYVEHSVRY QCKNYYKLRT EGDGVYTLNN EKQWINKAVG DKLPECEAVC GKPKNPANPV QRILGGHLDA KGSFPWQAKM VSHHNLTTGA TLINEQWLLT TAKNLFLNHS ENATAKDIAP TLTLYVGKKQ ...String:
MSALGAVIAL LLWGQLFAVD SGNDVTDIAD DGCPKPPEIA HGYVEHSVRY QCKNYYKLRT EGDGVYTLNN EKQWINKAVG DKLPECEAVC GKPKNPANPV QRILGGHLDA KGSFPWQAKM VSHHNLTTGA TLINEQWLLT TAKNLFLNHS ENATAKDIAP TLTLYVGKKQ LVEIEKVVLH PNYSQVDIGL IKLKQKVSVN ERVMPICLPS KDYAEVGRVG YVSGWGRNAN FKFTDHLKYV MLPVADQDQC IRHYEGSTVP EKKTPKSPVG VQPILNEHTF CAGMSKYQED TCYGDAGSAF AVHDLEEDTW YATGILSFDK SCAVAEYGVY VKVTSIQDWV QKTIAEN

UniProtKB: Haptoglobin

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Macromolecule #7: HBA1

MacromoleculeName: HBA1 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP AVHASLDKFL ASVSTVLTSK YR

UniProtKB: Hemoglobin subunit alpha

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Macromolecule #8: HBB

MacromoleculeName: HBB / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG KEFTPPVQAA YQKVVAGVAN ALAHKYH

UniProtKB: Hemoglobin subunit beta

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Macromolecule #9: HP

MacromoleculeName: HP / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSALGAVIAL LLWGQLFAVD SGNDVTDIAD DGCPKPPEIA HGYVEHSVRY QCKNYYKLRT EGDGVYTLNN EKQWINKAVG DKLPECEAVC GKPKNPANPV QRILGGHLDA KGSFPWQAKM VSHHNLTTGA TLINEQWLLT TAKNLFLNHS ENATAKDIAP TLTLYVGKKQ ...String:
MSALGAVIAL LLWGQLFAVD SGNDVTDIAD DGCPKPPEIA HGYVEHSVRY QCKNYYKLRT EGDGVYTLNN EKQWINKAVG DKLPECEAVC GKPKNPANPV QRILGGHLDA KGSFPWQAKM VSHHNLTTGA TLINEQWLLT TAKNLFLNHS ENATAKDIAP TLTLYVGKKQ LVEIEKVVLH PNYSQVDIGL IKLKQKVSVN ERVMPICLPS KDYAEVGRVG YVSGWGRNAN FKFTDHLKYV MLPVADQDQC IRHYEGSTVP EKKTPKSPVG VQPILNEHTF CAGMSKYQED TCYGDAGSAF AVHDLEEDTW YATGILSFDK SCAVAEYGVY VKVTSIQDWV QKTIAEN

UniProtKB: Haptoglobin

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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

Concentration0.1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2709108
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 245961
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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