[English] 日本語
Yorodumi
- EMDB-36940: Human Fc epsilon RI in complex with mIgE Fc (TMD disordered) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36940
TitleHuman Fc epsilon RI in complex with mIgE Fc (TMD disordered)
Map datamain map(sharpened)
Sample
  • Complex: Human Fc epsilon RI in complex with mIgE Fc
    • Protein or peptide: IgE Fc
    • Protein or peptide: FCER1A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIgE / high-affinity IgE receptor / allergy / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsZhang Z / Yui M / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Signal / Year: 2024
Title: Architecture of the high-affinity immunoglobulin E receptor.
Authors: Zhikuan Zhang / Moeko Yui / Umeharu Ohto / Toshiyuki Shimizu /
Abstract: The high-affinity immunoglobulin E (IgE) receptor (FcεRI) drives type I hypersensitivity in response to allergen-specific IgE. FcεRI is a multimeric complex typically composed of one α, one β, ...The high-affinity immunoglobulin E (IgE) receptor (FcεRI) drives type I hypersensitivity in response to allergen-specific IgE. FcεRI is a multimeric complex typically composed of one α, one β, and two disulfide-linked γ subunits. The α subunit binds to the fragment crystallizable (Fc) region of IgE (Fcε), whereas the β and γ subunits mediate signaling through their intracellular immunoreceptor tyrosine-based activation motifs (ITAMs). Here, we report cryo-electron microscopy (cryo-EM) structures of the apo state of FcεRI and of FcεRI bound to Fcε. At the transmembrane domain (TMD), the α and γ subunits associate to form a tightly packed, three-helix bundle (αγ bundle) with pseudo-threefold symmetry through extensive hydrophobic and polar interactions. The αγ bundle further assembles with the β subunit to complete the TMD, from which multiple ITAMs might extend into the cytoplasm for downstream signaling. The apo mouse FcεRI essentially forms an identical structure to that of the Fcε-bound sensitized form, suggesting that the binding of Fcε to FcεRI does not alter the overall conformation of the receptor. Furthermore, the juxtamembrane interaction between the extracellular domains (ECDs) of mouse FcεRIα and FcεRIβ is not observed between their human counterparts, which implies potential species-specific differences in receptor stability and activation. Our findings provide a framework for understanding the general structural principles underlying Fc receptor assembly, the signaling mechanism underlying type I hypersensitivity, and the design of efficient antiallergic therapeutics.
History
DepositionJul 27, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36940.png

Downloads & links

-
Map

FileDownload / File: emd_36940.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map(sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 160 pix.
= 265.6 Å		1.66 Å/pix.
x 160 pix.
= 265.6 Å		1.66 Å/pix.
x 160 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.0102687 - 4.22871
Average (Standard dev.)0.0007354675 (±0.057144523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_36940_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_36940_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_36940_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human Fc epsilon RI in complex with mIgE Fc

EntireName: Human Fc epsilon RI in complex with mIgE Fc
Components
  • Complex: Human Fc epsilon RI in complex with mIgE Fc
    • Protein or peptide: IgE Fc
    • Protein or peptide: FCER1A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Human Fc epsilon RI in complex with mIgE Fc

SupramoleculeName: Human Fc epsilon RI in complex with mIgE Fc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: IgE Fc

MacromoleculeName: IgE Fc / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.369723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METGLRWLLL VAVLKGVQCV RPVNITDPTL ELLHSSCDPN AFHSTIQLYC FIYGHILNDV SVSWLMDDRE ITDTLAQTVL IKEEGKLAS TCSKLNITEQ QWMSESTFTC KVTSQGVDYL AHTRRCPDHE PRGVITYLIP PSPLDLYQNG APKLTCLVVD L ESEKNVNV ...String:
METGLRWLLL VAVLKGVQCV RPVNITDPTL ELLHSSCDPN AFHSTIQLYC FIYGHILNDV SVSWLMDDRE ITDTLAQTVL IKEEGKLAS TCSKLNITEQ QWMSESTFTC KVTSQGVDYL AHTRRCPDHE PRGVITYLIP PSPLDLYQNG APKLTCLVVD L ESEKNVNV TWNQEKKTSV SASQWYTKHH NNATTSITSI LPVVAKDWIE GYGYQCIVDH PDFPKPIVRS ITKTPGQRSA PE VYVFPPP EEESEDKRTL TCLIQNFFPE DISVQWLGDG KLISNSQHST TTPLKSNGSN QGFFIFSRLE VAKTLWTQRK QFT CQVIHE ALQKPRKLEK TISTSLGNTS LRPSHHHHHH

-
Macromolecule #2: FCER1A

MacromoleculeName: FCER1A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.578768 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPAMESPTL LCVALLFFAP DGVLAVPQKP KVSLNPPWNR IFKGENVTLT CNGNNFFEVS STKWFHNGSL SEETNSSLNI VNAKFEDSG EYKCQHQQVN ESEPVYLEVF SDWLLLQASA EVVMEGQPLF LRCHGWRNWD VYKVIYYKDG EALKYWYENH N ISITNATV ...String:
MAPAMESPTL LCVALLFFAP DGVLAVPQKP KVSLNPPWNR IFKGENVTLT CNGNNFFEVS STKWFHNGSL SEETNSSLNI VNAKFEDSG EYKCQHQQVN ESEPVYLEVF SDWLLLQASA EVVMEGQPLF LRCHGWRNWD VYKVIYYKDG EALKYWYENH N ISITNATV EDSGTYYCTG KVWQLDYESE PLNITVIKAP REKYWLQFFI PLLVVILFAV DTGLFISTQQ QVTFLLKIKR TR KGFRLLN PHPKPNPKNN ENLYFQGDYK DDDDKHHHHH HHH

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166766
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more