[English] 日本語
Yorodumi
- EMDB-49208: Consensus map of the autoinhibitory unliganded CD163 trimer (map A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49208
TitleConsensus map of the autoinhibitory unliganded CD163 trimer (map A)
Map dataCD163_Trimer_Consensus_Map_A_sharpen
Sample
  • Complex: CD163 trimer
    • Protein or peptide: CD163
    • Protein or peptide: CD163
    • Protein or peptide: CD163
KeywordsCD163 / M130 / Scavenger receptor / 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: 3.0 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

-
Structure visualization

Supplemental images

emd_49208.png

Downloads & links

-
Map

FileDownload / File: emd_49208.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCD163_Trimer_Consensus_Map_A_sharpen
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: 0.8
Minimum - Maximum-4.8579683 - 7.5637217
Average (Standard dev.)0.00017784903 (±0.09859459)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_49208_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CD163 Trimer Consensus half map 1

Fileemd_49208_half_map_1.map
AnnotationCD163_Trimer_Consensus_half_map_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CD163 Trimer Consensus half map 2

Fileemd_49208_half_map_2.map
AnnotationCD163_Trimer_Consensus_half_map_2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CD163 trimer

EntireName: CD163 trimer
Components
  • Complex: CD163 trimer
    • Protein or peptide: CD163
    • Protein or peptide: CD163
    • Protein or peptide: CD163

-
Supramolecule #1: CD163 trimer

SupramoleculeName: CD163 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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: 40.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4184104
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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 391535
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more