[English] 日本語
Yorodumi
- EMDB-40567: Structure of human SIgA1 in complex with human CD89 (FcaR1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40567
TitleStructure of human SIgA1 in complex with human CD89 (FcaR1)
Map data
Sample
  • Complex: human SIgA1 in complex with human CD89 (FcaR1)
    • Protein or peptide: Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Secretory component
    • Protein or peptide: Immunoglobulin alpha Fc receptor
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSecretory immunoglobulin A / SIgA / IgA / CD89 / FcaR1 / IgA Fc receptor / protein complex / IMMUNE SYSTEM
Function / homology
Function and homology information


IgA receptor activity / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / cellular response to interferon-alpha / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / Fc receptor signaling pathway ...IgA receptor activity / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / cellular response to interferon-alpha / dimeric IgA immunoglobulin complex / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / Fc receptor signaling pathway / secretory IgA immunoglobulin complex / immune response-regulating signaling pathway / IgA binding / positive regulation of neutrophil apoptotic process / IgA immunoglobulin complex / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / neutrophil activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / cellular response to interleukin-6 / neutrophil mediated immunity / IgG immunoglobulin complex / immunoglobulin receptor binding / azurophil granule membrane / immunoglobulin complex, circulating / receptor clustering / positive regulation of respiratory burst / tertiary granule membrane / humoral immune response / ficolin-1-rich granule membrane / complement activation, classical pathway / Scavenging of heme from plasma / specific granule membrane / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / cellular response to type II interferon / epidermal growth factor receptor signaling pathway / antibacterial humoral response / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / protein-containing complex assembly / protein-macromolecule adaptor activity / blood microparticle / adaptive immune response / receptor complex / immune response / innate immune response / Neutrophil degranulation / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / : / : / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Immunoglobulin J chain / Immunoglobulin J chain / : / : / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin J chain / Polymeric immunoglobulin receptor / Immunoglobulin heavy constant alpha 1 / Immunoglobulin alpha Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu Q / Stadtmueller BM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI165570 United States
CitationJournal: Nat Commun / Year: 2023
Title: SIgA structures bound to Streptococcus pyogenes M4 and human CD89 provide insights into host-pathogen interactions.
Authors: Qianqiao Liu / Beth M Stadtmueller /
Abstract: Immunoglobulin (Ig) A functions as monomeric IgA in the serum and Secretory (S) IgA in mucosal secretions. Host IgA Fc receptors (FcαRs), including human FcαR1/CD89, mediate IgA effector functions; ...Immunoglobulin (Ig) A functions as monomeric IgA in the serum and Secretory (S) IgA in mucosal secretions. Host IgA Fc receptors (FcαRs), including human FcαR1/CD89, mediate IgA effector functions; however, human pathogen Streptococcus pyogenes has evolved surface-protein virulence factors, including M4, that also engage the CD89-binding site on IgA. Despite human mucosa serving as a reservoir for pathogens, SIgA interactions with CD89 and M4 remain poorly understood. Here we report cryo-EM structures of M4-SIgA and CD89-SIgA complexes, which unexpectedly reveal different SIgA-binding stoichiometry for M4 and CD89. Structural data, supporting experiments, and modeling indicate that copies of SIgA bound to S. pyogenes M4 will adopt similar orientations on the bacterium surface and leave one host FcαR binding site open. Results suggest unappreciated functional consequences associated with SIgA binding to host and bacterial FcαRs relevant to understanding host-microbe co-evolution, IgA effector functions and improving the outcomes of group A Streptococcus infection.
History
DepositionApr 20, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40567.png

Downloads & links

-
Map

FileDownload / File: emd_40567.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.86661124 - 1.3258854
Average (Standard dev.)-0.00016093526 (±0.016548203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 361.68002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_40567_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40567_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human SIgA1 in complex with human CD89 (FcaR1)

EntireName: human SIgA1 in complex with human CD89 (FcaR1)
Components
  • Complex: human SIgA1 in complex with human CD89 (FcaR1)
    • Protein or peptide: Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Secretory component
    • Protein or peptide: Immunoglobulin alpha Fc receptor
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: human SIgA1 in complex with human CD89 (FcaR1)

SupramoleculeName: human SIgA1 in complex with human CD89 (FcaR1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Immunoglobulin heavy constant alpha 1

MacromoleculeName: Immunoglobulin heavy constant alpha 1 / type: protein_or_peptide / ID: 1
Details: The sequence of the Fab region is not included due to legal reasons.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.687488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASPTSPKVFP LSLCSTQPDG NVVIACLVQG FFPQEPLSVT WSESGQGVTA RNFPPSQDAS GDLYTTSSQL TLPATQCLAG KSVTCHVKH YTNPSQDVTV PCPVPSTPPT PSPSTPPTPS PSCCHPRLSL HRPALEDLLL GSEANLTCTL TGLRDASGVT F TWTPSSGK ...String:
ASPTSPKVFP LSLCSTQPDG NVVIACLVQG FFPQEPLSVT WSESGQGVTA RNFPPSQDAS GDLYTTSSQL TLPATQCLAG KSVTCHVKH YTNPSQDVTV PCPVPSTPPT PSPSTPPTPS PSCCHPRLSL HRPALEDLLL GSEANLTCTL TGLRDASGVT F TWTPSSGK SAVQGPPERD LCGCYSVSSV LPGCAEPWNH GKTFTCTAAY PESKTPLTAT LSKSGNTFRP EVHLLPPPSE EL ALNELVT LTCLARGFSP KDVLVRWLQG SQELPREKYL TWASRQEPSQ GTTTFAVTSI LRVAAEDWKK GDTFSCMVGH EAL PLAFTQ KTIDRLAGKP THVNVSVVMA EVDGTCY

UniProtKB: Immunoglobulin heavy constant alpha 1

-
Macromolecule #2: Secretory component

MacromoleculeName: Secretory component / type: protein_or_peptide / ID: 2 / Details: secretory component / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.095578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KSPIFGPEEV NSVEGNSVSI TCYYPPTSVN RHTRKYWCRQ GARGGCITLI SSEGYVSSKY AGRANLTNFP ENGTFVVNIA QLSQDDSGR YKCGLGINSR GLSFDVSLEV SQGPGLLNDT KVYTVDLGRT VTINCPFKTE NAQKRKSLYK QIGLYPVLVI D SSGYVNPN ...String:
KSPIFGPEEV NSVEGNSVSI TCYYPPTSVN RHTRKYWCRQ GARGGCITLI SSEGYVSSKY AGRANLTNFP ENGTFVVNIA QLSQDDSGR YKCGLGINSR GLSFDVSLEV SQGPGLLNDT KVYTVDLGRT VTINCPFKTE NAQKRKSLYK QIGLYPVLVI D SSGYVNPN YTGRIRLDIQ GTGQLLFSVV INQLRLSDAG QYLCQAGDDS NSNKKNADLQ VLKPEPELVY EDLRGSVTFH CA LGPEVAN VAKFLCRQSS GENCDVVVNT LGKRAPAFEG RILLNPQDKD GSFSVVITGL RKEDAGRYLC GAHSDGQLQE GSP IQAWQL FVNEESTIPR SPTVVKGVAG GSVAVLCPYN RKESKSIKYW CLWEGAQNGR CPLLVDSEGW VKAQYEGRLS LLEE PGNGT FTVILNQLTS RDAGFYWCLT NGDTLWRTTV EIKIIEGEPN LKVPGNVTAV LGETLKVPCH FPCKFSSYEK YWCKW NNTG CQALPSQDEG PSKAFVNCDE NSRLVSLTLN LVTRADEGWY WCGVKQGHFY GETAAVYVAV EERHHHHHH

UniProtKB: Polymeric immunoglobulin receptor

-
Macromolecule #3: Immunoglobulin alpha Fc receptor

MacromoleculeName: Immunoglobulin alpha Fc receptor / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.615742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QEGDFPMPFI SAKSSPVIPL DGSVKIQCQA IREAYLTQLM IIKNSTYREI GRRLKFWNET DPEFVIDHMD ANKAGRYQCQ YRIGHYRFR YSDTLELVVT GLYGKPFLSA DRGLVLMPGE NISLTCSSAH IPFDRFSLAK EGELSLPQHQ SGEHPANFSL G PVDLNVSG ...String:
QEGDFPMPFI SAKSSPVIPL DGSVKIQCQA IREAYLTQLM IIKNSTYREI GRRLKFWNET DPEFVIDHMD ANKAGRYQCQ YRIGHYRFR YSDTLELVVT GLYGKPFLSA DRGLVLMPGE NISLTCSSAH IPFDRFSLAK EGELSLPQHQ SGEHPANFSL G PVDLNVSG IYRCYGWYNR SPYLWSFPSN ALELVVTAID GRAHHHHHH

UniProtKB: Immunoglobulin alpha Fc receptor

-
Macromolecule #4: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.611458 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QEDERIVLVD NKCKCARITS RIIRSSEDPN EDIVERNIRI IVPLNNRENI SDPTSPLRTR FVYHLSDLCK KCDPTEVELD NQIVTATQS NICDEDSATE TCYTYDRNKC YTAVVPLVYG GETKMVETAL TPDACYPD

UniProtKB: Immunoglobulin J chain

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 71.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ue7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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