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- EMDB-19896: Structure of IgE HMM5 bound to FceRIa cryo-EM class 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-19896
TitleStructure of IgE HMM5 bound to FceRIa cryo-EM class 5
Map dataclass05 map
Sample
  • Complex: complex of IgE HMM5 and the ectodomain of FceRIa
    • Protein or peptide: IgE HMM5 heavy chain
    • Protein or peptide: IgE HMM5 light chain
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIgE / Fc receptor / allergy / antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / Fc epsilon receptor (FCERI) signaling / type 2 immune response / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization ...high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / Fc epsilon receptor (FCERI) signaling / type 2 immune response / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
High affinity immunoglobulin epsilon receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 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: Biorxiv / Year: 2023
Title: The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy
Authors: Jensen RK / Miehe M / Gandini R / Jorgensen MH / Spillner E / Andersen GR
History
DepositionMar 20, 2024-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19896.png

Downloads & links

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Map

FileDownload / File: emd_19896.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationclass05 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.6 Å		0.83 Å/pix.
x 400 pix.
= 331.6 Å		0.83 Å/pix.
x 400 pix.
= 331.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.22359088 - 1.1817563
Average (Standard dev.)0.023961877 (±0.04713368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: class 05 halfmap A

Fileemd_19896_half_map_1.map
Annotationclass 05 halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: class 05 halfmap B

Fileemd_19896_half_map_2.map
Annotationclass 05 halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex of IgE HMM5 and the ectodomain of FceRIa

EntireName: complex of IgE HMM5 and the ectodomain of FceRIa
Components
  • Complex: complex of IgE HMM5 and the ectodomain of FceRIa
    • Protein or peptide: IgE HMM5 heavy chain
    • Protein or peptide: IgE HMM5 light chain
    • Protein or peptide: High affinity immunoglobulin epsilon receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: complex of IgE HMM5 and the ectodomain of FceRIa

SupramoleculeName: complex of IgE HMM5 and the ectodomain of FceRIa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: IgE HMM5 heavy chain

MacromoleculeName: IgE HMM5 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.203508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSLEESGGRL VTPGTPLTLT CTVSGFSLST YNIHWVRQAP GKGLEWIGVI DTGGGTYFAS WAKGRFAISK TSSTTVDLKM TSLTAADTA TYFCAKGFDY SASTNLWGPG TLVTISSAST QSPSVFPLTR CCKNIPSNAT SVTLGCLATG YFPEPVMVTW D TGSLNGTT ...String:
QSLEESGGRL VTPGTPLTLT CTVSGFSLST YNIHWVRQAP GKGLEWIGVI DTGGGTYFAS WAKGRFAISK TSSTTVDLKM TSLTAADTA TYFCAKGFDY SASTNLWGPG TLVTISSAST QSPSVFPLTR CCKNIPSNAT SVTLGCLATG YFPEPVMVTW D TGSLNGTT MTLPATTLTL SGHYATISLL TVSGAWAKQM FTCRVAHTPS STDWVDNKTF SVCSRDFTPP TVKILQSSCD GG GHFPPTI QLLCLVSGYT PGTINITWLE DGQVMDVDLS TASTTQEGEL ASTQSELTLS QKHWLSDRTY TCQVTYQGHT FED STKKCA DSNPRGVSAY LSRPSPFDLF IRKSPTITCL VVDLAPSKGT VNLTWSRASG KPVNHSTRKE EKQRNGTLTV TSTL PVGTR DWIEGETYQC RVTHPHLPRA LMRSTTKTSG PRAAPEVYAF ATPEWPGSRD KRTLACLIQN FMPEDISVQW LHNEV QLPD ARHSTTQPRK TKGSGFFVFS RLEVTRAEWE QKDEFICRAV HEAASPSQTV QRAVSSVNPG KHHHHHH

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Macromolecule #2: IgE HMM5 light chain

MacromoleculeName: IgE HMM5 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.384795 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELDMTQTPSS VSAPVGGSVT INCQSSQSVY GNNYLAWYQQ KAGQPPKLLI YRASTLASGA PSRFKGSGSG TQFTLTISDL ESDDAATYY CLGYYNGVIN VFGGGTNVEI KRTVGAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
ELDMTQTPSS VSAPVGGSVT INCQSSQSVY GNNYLAWYQQ KAGQPPKLLI YRASTLASGA PSRFKGSGSG TQFTLTISDL ESDDAATYY CLGYYNGVIN VFGGGTNVEI KRTVGAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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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

UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: SPOTITON

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18410
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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