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- EMDB-30008: Cryo-EM structure of human secretory immunoglobulin A in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30008
TitleCryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal domain of SpsA
Map data
Sample
  • Complex: Quadruple complex of human secretory immunoglobulin A with the N-terminal domain of SpsA
    • Protein or peptide: Interleukin-2,Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Immunoglobulin J chain
    • Protein or peptide: Polymeric immunoglobulin receptor
    • Protein or peptide: SigA binding protein
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 / dimeric IgA immunoglobulin complex / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / polymeric immunoglobulin binding / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / positive regulation of plasma cell differentiation ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / kappa-type opioid receptor binding / dimeric IgA immunoglobulin complex / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / polymeric immunoglobulin binding / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / positive regulation of plasma cell differentiation / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / Fc receptor signaling pathway / IgA binding / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / IgA immunoglobulin complex / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / natural killer cell activation / activated T cell proliferation / positive regulation of regulatory T cell differentiation / protein kinase C-activating G protein-coupled receptor signaling pathway / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of dendritic spine development / azurophil granule membrane / receptor clustering / positive regulation of activated T cell proliferation / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / positive regulation of interleukin-17 production / positive regulation of respiratory burst / humoral immune response / positive regulation of immunoglobulin production / T cell differentiation / Scavenging of heme from plasma / Interleukin receptor SHC signaling / complement activation, classical pathway / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / antigen binding / negative regulation of protein phosphorylation / 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 inflammatory response / positive regulation of type II interferon production / protein-macromolecule adaptor activity / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / antibacterial humoral response / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / protein-containing complex assembly / blood microparticle / response to ethanol / transcription by RNA polymerase II / adaptive immune response / receptor complex / cell adhesion / immune response / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
RICH domain / RICH domain superfamily / RICH domain / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Immunoglobulin J chain / Immunoglobulin J chain ...RICH domain / RICH domain superfamily / RICH domain / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Immunoglobulin J chain / Immunoglobulin J chain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / YSIRK type signal peptide / Four-helical cytokine-like, core / YSIRK Gram-positive signal peptide / 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
SigA binding protein / Immunoglobulin J chain / Polymeric immunoglobulin receptor / Immunoglobulin heavy constant alpha 1 / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Streptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsWang Y / Wang G / Li Y / Xiao J
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 12, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00863
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00863
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lxw
  • Surface level: 0.00863
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30008.png

Downloads & links

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Map

FileDownload / File: emd_30008.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.00863 / Movie #1: 0.00863
Minimum - Maximum-0.08623363 - 0.11885852
Average (Standard dev.)0.00010553111 (±0.0021591817)
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-0.0860.1190.000

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Supplemental data

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Mask #1

Fileemd_30008_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30008_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30008_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Quadruple complex of human secretory immunoglobulin A with the N-...

EntireName: Quadruple complex of human secretory immunoglobulin A with the N-terminal domain of SpsA
Components
  • Complex: Quadruple complex of human secretory immunoglobulin A with the N-terminal domain of SpsA
    • Protein or peptide: Interleukin-2,Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Immunoglobulin J chain
    • Protein or peptide: Polymeric immunoglobulin receptor
    • Protein or peptide: SigA binding protein

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Supramolecule #1: Quadruple complex of human secretory immunoglobulin A with the N-...

SupramoleculeName: Quadruple complex of human secretory immunoglobulin A with the N-terminal domain of SpsA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

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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

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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

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Macromolecule #4: SigA binding protein

MacromoleculeName: SigA binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 36.311113 KDa
Recombinant expressionOrganism: Escherichia phage Ecwhy_1 (virus)
SequenceString: MGSHHHHHHH HGSDYDIPTT ENLYFQGSEF TENEGSTQAA TFSNMANKSQ TEQGEINIER DKAKTAVSEY KEKKVSEIYT KLERDRHKD TVDLVNKLQE IKNEYLNKIV QSTSKTEIQG LITTSRSKLD EAVSKYKKAP SSSSSSGSST KPEASDTAKP N KPTELEKK ...String:
MGSHHHHHHH HGSDYDIPTT ENLYFQGSEF TENEGSTQAA TFSNMANKSQ TEQGEINIER DKAKTAVSEY KEKKVSEIYT KLERDRHKD TVDLVNKLQE IKNEYLNKIV QSTSKTEIQG LITTSRSKLD EAVSKYKKAP SSSSSSGSST KPEASDTAKP N KPTELEKK VAEAEKKVEE AKKKAKDQKE EDYRNYPTIT YKTLELEIAE SDVEVKKAEL ELVKEEAKEP RNEEKVKQAK AK VESEETE ATRLEKIKTD RKKAEEEAKR KAAEEDKVKE KPAEQQAEED YARRSEEEYN RLTQQQPPKT EKPAQPSTPK

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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

Concentration0.2 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.74 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280791
FSC plot (resolution estimation)

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