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- PDB-6lxw: Cryo-EM structure of human secretory immunoglobulin A in complex ... -

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Basic information

Entry
Database: PDB / ID: 6lxw
TitleCryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal domain of SpsA
Components
  • Immunoglobulin J chain
  • Interleukin-2,Immunoglobulin heavy constant alpha 1
  • Polymeric immunoglobulin receptor
  • SigA binding protein
KeywordsIMMUNE SYSTEM / immunoglobulin / dimer / transcytosis / secreted
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 / positive regulation of isotype switching to IgG isotypes / leukocyte activation involved in immune response / 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 / adaptive immune response / transcription by RNA polymerase II / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsWang, Y. / Wang, G. / Li, Y. / Xiao, J.
Funding support China, 1items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Interleukin-2,Immunoglobulin heavy constant alpha 1
B: Interleukin-2,Immunoglobulin heavy constant alpha 1
C: Interleukin-2,Immunoglobulin heavy constant alpha 1
D: Interleukin-2,Immunoglobulin heavy constant alpha 1
J: Immunoglobulin J chain
P: Polymeric immunoglobulin receptor
S: SigA binding protein


Theoretical massNumber of molelcules
Total (without water)244,6267
Polymers244,6267
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20420 Å2
ΔGint-111 kcal/mol
Surface area75950 Å2

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Components

#1: Antibody
Interleukin-2,Immunoglobulin heavy constant alpha 1 / IL-2 / T-cell growth factor / TCGF / Ig alpha-1 chain C region / Ig alpha-1 chain C region BUR / Ig ...IL-2 / T-cell growth factor / TCGF / Ig alpha-1 chain C region / Ig alpha-1 chain C region BUR / Ig alpha-1 chain C region TRO


Mass: 31445.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2, IGHA1 / Production host: Homo sapiens (human) / References: UniProt: P60568, UniProt: P01876
#2: Protein Immunoglobulin J chain / Joining chain of multimeric IgA and IgM


Mass: 19225.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JCHAIN, IGCJ, IGJ / Production host: Homo sapiens (human) / References: UniProt: P01591
#3: Protein Polymeric immunoglobulin receptor / / Poly-Ig receptor / Hepatocellular carcinoma-associated protein TB6


Mass: 63306.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIGR / Production host: Homo sapiens (human) / References: UniProt: P01833
#4: Protein SigA binding protein


Mass: 36311.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: spsA / Production host: Escherichia phage Ecwhy_1 (virus) / References: UniProt: O33753

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Quadruple complex of human secretory immunoglobulin A with the N-terminal domain of SpsA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 59.74 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280791 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01512565
ELECTRON MICROSCOPYf_angle_d1.24417096
ELECTRON MICROSCOPYf_dihedral_angle_d8.0037578
ELECTRON MICROSCOPYf_chiral_restr0.071962
ELECTRON MICROSCOPYf_plane_restr0.0092195

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