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- EMDB-30004: Cryo-EM structure of human secretory immunoglobulin A -

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Basic information

Entry
Database: EMDB / ID: EMD-30004
TitleCryo-EM structure of human secretory immunoglobulin A
Map data
Sample
  • Complex: Ternary complex of IgA-Fc with the J chain and pIgR/SC
    • Protein or peptide: Interleukin-2,Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Immunoglobulin J chain
    • Protein or peptide: Polymeric immunoglobulin receptor
Keywordsimmunoglobulin / dimer / transcytosis / secreted / IMMUNE SYSTEM
Function / homology
Function and homology information


polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / kappa-type opioid receptor binding / polymeric immunoglobulin binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / dimeric IgA immunoglobulin complex / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / kappa-type opioid receptor binding / polymeric immunoglobulin binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / dimeric IgA immunoglobulin complex / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of lymphocyte proliferation / response to tacrolimus / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / IgA binding / IgA immunoglobulin complex / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / glomerular filtration / detection of chemical stimulus involved in sensory perception of bitter taste / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / cell surface receptor signaling pathway via STAT / kinase activator activity / IgG immunoglobulin complex / natural killer cell activation / Interleukin-2 signaling / positive regulation of regulatory T cell differentiation / immunoglobulin receptor binding / azurophil granule membrane / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / negative regulation of B cell apoptotic process / immunoglobulin complex, circulating / receptor clustering / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / positive regulation of respiratory burst / humoral immune response / T cell differentiation / Interleukin receptor SHC signaling / complement activation, classical pathway / Scavenging of heme from plasma / antigen binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of B cell proliferation / cytokine activity / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / growth factor activity / epidermal growth factor receptor signaling pathway / negative regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of inflammatory response / antibacterial humoral response / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / protein-containing complex assembly / protein-macromolecule adaptor activity / response to ethanol / blood microparticle / adaptive immune response / transcription by RNA polymerase II / receptor complex / cell adhesion / immune response / G protein-coupled receptor signaling pathway / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Immunoglobulin J chain / Immunoglobulin J chain / : / Four-helical cytokine-like, core / Immunoglobulin ...Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Immunoglobulin J chain / Immunoglobulin J chain / : / Four-helical cytokine-like, core / 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 / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsWang Y / Wang G
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Res / Year: 2020
Title: Structural insights into secretory immunoglobulin A and its interaction with a pneumococcal adhesin.
Authors: Yuxin Wang / Guopeng Wang / Yaxin Li / Qinyu Zhu / Hao Shen / Ning Gao / Junyu Xiao /
Abstract: Secretory Immunoglobulin A (SIgA) is the most abundant antibody at the mucosal surface. It possesses two additional subunits besides IgA: the joining chain (J-chain) and secretory component (SC). SC ...Secretory Immunoglobulin A (SIgA) is the most abundant antibody at the mucosal surface. It possesses two additional subunits besides IgA: the joining chain (J-chain) and secretory component (SC). SC is the ectodomain of the polymeric immunoglobulin receptor (pIgR), which functions to transport IgA to the mucosa. How the J-chain and pIgR/SC facilitate the assembly and secretion of SIgA remains incompletely understood. Furthermore, during the infection of Streptococcus pneumoniae, the pneumococcal adhesin SpsA hijacks pIgR/SC and SIgA to gain entry to human cells and evade host defense. How SpsA targets pIgR/SC and SIgA also remains elusive. Here we report a cryo-electron microscopy structure of the Fc region of IgA1 (Fcα) in complex with the J-chain and SC (Fcα-J-SC), which reveals the organization principle of SIgA. We also present a structure of Fcα-J-SC complexed with SpsA, which uncovers the specific interactions between SpsA and human pIgR/SC. These results advance the molecular understanding of SIgA and shed light on S. pneumoniae pathogenesis.
History
DepositionFeb 10, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00935
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00935
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lx3
  • Surface level: 0.00935
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30004.png

Downloads & links

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Map

FileDownload / File: emd_30004.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00935 / Movie #1: 0.00935
Minimum - Maximum-0.09906162 - 0.16208594
Average (Standard dev.)0.0000920879 (±0.0025598092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8280.8280.828
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z264.960264.960264.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0990.1620.000

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Supplemental data

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Mask #1

Fileemd_30004_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30004_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30004_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ternary complex of IgA-Fc with the J chain and pIgR/SC

EntireName: Ternary complex of IgA-Fc with the J chain and pIgR/SC
Components
  • Complex: Ternary complex of IgA-Fc with the J chain and pIgR/SC
    • Protein or peptide: Interleukin-2,Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Immunoglobulin J chain
    • Protein or peptide: Polymeric immunoglobulin receptor

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Supramolecule #1: Ternary complex of IgA-Fc with the J chain and pIgR/SC

SupramoleculeName: Ternary complex of IgA-Fc with the J chain and pIgR/SC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interleukin-2,Immunoglobulin heavy constant alpha 1

MacromoleculeName: Interleukin-2,Immunoglobulin heavy constant alpha 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.445693 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS ARIHMSAWSH PQFEKGGGSG GGSGGSAWSH PQFEKIDTTC CHPRLSLHRP ALEDLLLGSE ANLTCTLTG LRDASGVTFT WTPSSGKSAV QGPPERDLCG CYSVSSVLPG CAEPWNHGKT FTCTAAYPES KTPLTATLSK S GNTFRPEV ...String:
MYRMQLLSCI ALSLALVTNS ARIHMSAWSH PQFEKGGGSG GGSGGSAWSH PQFEKIDTTC CHPRLSLHRP ALEDLLLGSE ANLTCTLTG LRDASGVTFT WTPSSGKSAV QGPPERDLCG CYSVSSVLPG CAEPWNHGKT FTCTAAYPES KTPLTATLSK S GNTFRPEV HLLPPPSEEL ALNELVTLTC LARGFSPKDV LVRWLQGSQE LPREKYLTWA SRQEPSQGTT TFAVTSILRV AA EDWKKGD TFSCMVGHEA LPLAFTQKTI DRLAGKPTHV NVSVVMAEVD GTCY

UniProtKB: Interleukin-2, Immunoglobulin heavy constant alpha 1

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Macromolecule #2: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.225762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MKNHLLFWGV LAVFIKAVHV KAQEDERIVL VDNKCKCARI TSRIIRSSED PNEDIVERNI RIIVPLNNRE NISDPTSPLR TRFVYHLSD LCKKCDPTEV ELDNQIVTAT QSNICDEDSA TETCYTYDRN KCYTAVVPLV YGGETKMVET ALTPDACYPD H HHHHHHH

UniProtKB: Immunoglobulin J chain

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Macromolecule #3: Polymeric immunoglobulin receptor

MacromoleculeName: Polymeric immunoglobulin receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.306336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLLFVLTCLL AVFPAISTKS PIFGPEEVNS VEGNSVSITC YYPPTSVNRH TRKYWCRQGA RGGCITLISS EGYVSSKYAG RANLTNFPE NGTFVVNIAQ LSQDDSGRYK CGLGINSRGL SFDVSLEVSQ GPGLLNDTKV YTVDLGRTVT INCPFKTENA Q KRKSLYKQ ...String:
MLLFVLTCLL AVFPAISTKS PIFGPEEVNS VEGNSVSITC YYPPTSVNRH TRKYWCRQGA RGGCITLISS EGYVSSKYAG RANLTNFPE NGTFVVNIAQ LSQDDSGRYK CGLGINSRGL SFDVSLEVSQ GPGLLNDTKV YTVDLGRTVT INCPFKTENA Q KRKSLYKQ IGLYPVLVID SSGYVNPNYT GRIRLDIQGT GQLLFSVVIN QLRLSDAGQY LCQAGDDSNS NKKNADLQVL KP EPELVYE DLRGSVTFHC ALGPEVANVA KFLCRQSSGE NCDVVVNTLG KRAPAFEGRI LLNPQDKDGS FSVVITGLRK EDA GRYLCG AHSDGQLQEG SPIQAWQLFV NEESTIPRSP TVVKGVAGGS VAVLCPYNRK ESKSIKYWCL WEGAQNGRCP LLVD SEGWV KAQYEGRLSL LEEPGNGTFT VILNQLTSRD AGFYWCLTNG DTLWRTTVEI KIIEGEPNLK VPGNVTAVLG ETLKV PCHF PCKFSSYEKY WCKWNNTGCQ ALPSQDEGPS KAFVNCDENS RLVSLTLNLV TRADEGWYWC GVKQGHFYGE TAAVYV AVE ERHHHHHHHH

UniProtKB: Polymeric immunoglobulin receptor

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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

Concentration0.3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 59.74 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 11.668 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 665589
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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