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- EMDB-16378: Structure of IgE bound to the ectodomain of FceRIa -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16378
TitleStructure of IgE bound to the ectodomain of FceRIa
Map dataconsensus map
Sample
  • Complex: IgE-FceRIa complex
    • Protein or peptide: Immunoglobulin heavy constant epsilon
    • Protein or peptide: Immunoglobulin kappa constant
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


high-affinity IgE receptor activity / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / IgD immunoglobulin complex / eosinophil degranulation / IgM immunoglobulin complex ...high-affinity IgE receptor activity / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / IgD immunoglobulin complex / eosinophil degranulation / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / macrophage activation / IgE binding / type 2 immune response / CD22 mediated BCR regulation / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / mast cell degranulation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / B cell proliferation / immunoglobulin receptor binding / macrophage differentiation / immunoglobulin mediated immune response / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / adaptive immune response / cell surface receptor signaling pathway / immune response / inflammatory response / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 kappa constant / Immunoglobulin heavy constant epsilon / High affinity immunoglobulin epsilon receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsAndersen GR / Jensen RK
Funding support Denmark, 3 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0052105 Denmark
LundbeckfondenR155-2015-2666 Denmark
Danish Council for Independent Research0135-00061B Denmark
CitationJournal: To Be Published
Title: Structure of IgE bound to the ectodomain of FceRIa
Authors: Andersen GR / Jensen RK
History
DepositionDec 20, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16378.png

Downloads & links

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Map

FileDownload / File: emd_16378.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 414.5 Å		1.04 Å/pix.
x 400 pix.
= 414.5 Å		1.04 Å/pix.
x 400 pix.
= 414.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1788036 - 3.256266
Average (Standard dev.)0.0006115489 (±0.05338386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 414.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B for consensus map

Fileemd_16378_half_map_1.map
Annotationhalf map B for consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A for consensus map

Fileemd_16378_half_map_2.map
Annotationhalf map A for consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IgE-FceRIa complex

EntireName: IgE-FceRIa complex
Components
  • Complex: IgE-FceRIa complex
    • Protein or peptide: Immunoglobulin heavy constant epsilon
    • Protein or peptide: Immunoglobulin kappa constant
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: IgE-FceRIa complex

SupramoleculeName: IgE-FceRIa complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Details: complex of IgE bound to the ectodomain of the FceRIa subunit
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Immunoglobulin heavy constant epsilon

MacromoleculeName: Immunoglobulin heavy constant epsilon / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.831613 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASTQSPSVFP LTRCCKNIPS NATSVTLGCL ATGYFPEPVM VTWDTGSLNG TTMTLPATTL TLSGHYATIS LLTVSGAWAK QMFTCRVAH TPSSTDWVDN KTFSVCSRDF TPPTVKILQS SCDGGGHFPP TIQLLCLVSG YTPGTINITW LEDGQVMDVD L STASTTQE ...String:
ASTQSPSVFP LTRCCKNIPS NATSVTLGCL ATGYFPEPVM VTWDTGSLNG TTMTLPATTL TLSGHYATIS LLTVSGAWAK QMFTCRVAH TPSSTDWVDN KTFSVCSRDF TPPTVKILQS SCDGGGHFPP TIQLLCLVSG YTPGTINITW LEDGQVMDVD L STASTTQE GELASTQSEL TLSQKHWLSD RTYTCQVTYQ GHTFEDSTKK CADSNPRGVS AYLSRPSPFD LFIRKSPTIT CL VVDLAPS KGTVNLTWSR ASGKPVNHST RKEEKQRNGT LTVTSTLPVG TRDWIEGETY QCRVTHPHLP RALMRSTTKT SGP RAAPEV YAFATPEWPG SRDKRTLACL IQNFMPEDIS VQWLHNEVQL PDARHSTTQP RKTKGSGFFV FSRLEVTRAE WEQK DEFIC RAVHEAASPS QTVQRAVSSV A

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Macromolecule #2: Immunoglobulin kappa constant

MacromoleculeName: Immunoglobulin kappa constant / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.763983 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RTVGAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit alpha

MacromoleculeName: High affinity immunoglobulin epsilon receptor subunit alpha
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.88007 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KPKVSLNPPW NRIFKGENVT LTCNGNNFFE VSSTKWFHNG SLSEETNSSL NIVNAKFEDS GEYKCQHQQV NESEPVYLEV FSDWLLLQA SAEVVMEGQP LFLRCHGWRN WDVYKVIYYK DGEALKYWYE NHNISITNAT VEDSGTYYCT GKVWQLDYES E PLNITVIK APR

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration3.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.16 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Stochastic gradient descent based model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 573328

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