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- EMDB-63783: Cryo-EM structure of human FcRL4 bound to IgA-Fc/J -

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Basic information

Entry
Database: EMDB / ID: EMD-63783
TitleCryo-EM structure of human FcRL4 bound to IgA-Fc/J
Map data
Sample
  • Complex: Ternary complex of IgA-Fc with the J-chain and FcRL4
    • Protein or peptide: Interleukin-2,Fc receptor-like protein 4
    • Protein or peptide: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsImmunoglobulin A / Fc receptor / FCRL4 / J-chain / IMMUNE SYSTEM
Function / homology
Function and homology information


response to tacrolimus / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / dimeric IgA immunoglobulin complex / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / secretory IgA immunoglobulin complex ...response to tacrolimus / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / dimeric IgA immunoglobulin complex / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / secretory IgA immunoglobulin complex / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of plasma cell differentiation / positive regulation of tissue remodeling / IgA binding / negative regulation of T-helper 17 cell differentiation / IgA immunoglobulin complex / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / glomerular filtration / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / activated T cell proliferation / cell surface receptor signaling pathway via STAT / Interleukin-2 signaling / natural killer cell activation / kinase activator activity / positive regulation of activated T cell proliferation / immunoglobulin complex, circulating / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / immunoglobulin receptor binding / IgG immunoglobulin complex / interleukin-2-mediated signaling pathway / positive regulation of immunoglobulin production / positive regulation of interleukin-17 production / positive regulation of dendritic spine development / positive regulation of respiratory burst / humoral immune response / T cell differentiation / complement activation, classical pathway / Interleukin receptor SHC signaling / Scavenging of heme from plasma / antigen binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of B cell proliferation / cytokine activity / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of inflammatory response / transmembrane signaling receptor activity / cell-cell signaling / antibacterial humoral response / carbohydrate binding / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / protein-containing complex assembly / blood microparticle / transcription by RNA polymerase II / phospholipase C-activating G protein-coupled receptor signaling pathway / adaptive immune response / response to ethanol / protein-macromolecule adaptor activity / cell surface receptor signaling pathway / cell adhesion / immune response / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Immunoglobulin J chain / Immunoglobulin J chain / : / Immunoglobulin domain / Four-helical cytokine-like, core ...Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Immunoglobulin J chain / Immunoglobulin J chain / : / Immunoglobulin domain / Four-helical cytokine-like, core / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 J chain / Immunoglobulin heavy constant alpha 1 / Interleukin-2 / Fc receptor-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang YX / Su C / Xiao JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: FcRL4 is an IgA receptor that primarily binds the joining chain
Authors: Wang YX / Su C / Xiao JY
History
DepositionMar 17, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63783.png

Downloads & links

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Map

FileDownload / File: emd_63783.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.2943848 - 1.8152767
Average (Standard dev.)-0.00007841925 (±0.024659075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63783_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63783_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of IgA-Fc with the J-chain and FcRL4

EntireName: Ternary complex of IgA-Fc with the J-chain and FcRL4
Components
  • Complex: Ternary complex of IgA-Fc with the J-chain and FcRL4
    • Protein or peptide: Interleukin-2,Fc receptor-like protein 4
    • Protein or peptide: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
    • Protein or peptide: Immunoglobulin J chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of IgA-Fc with the J-chain and FcRL4

SupramoleculeName: Ternary complex of IgA-Fc with the J-chain and FcRL4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interleukin-2,Fc receptor-like protein 4

MacromoleculeName: Interleukin-2,Fc receptor-like protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.055633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS ARIHAHKPVI SVHPPWTTFF KGERVTLTCN GFQFYATEKT TWYHRHYWGE KLTLTPGNTL EVRESGLYR CQARGSPRSN PVRLLFSSDS LILQAPYSVF EGDTLVLRCH RRRKEKLTAV KYTWNGNILS ISNKSWDLLI P QASSNNNG ...String:
MYRMQLLSCI ALSLALVTNS ARIHAHKPVI SVHPPWTTFF KGERVTLTCN GFQFYATEKT TWYHRHYWGE KLTLTPGNTL EVRESGLYR CQARGSPRSN PVRLLFSSDS LILQAPYSVF EGDTLVLRCH RRRKEKLTAV KYTWNGNILS ISNKSWDLLI P QASSNNNG NYRCIGYGDE NDVFRSNFKI IKIQELFPHP ELKATDSQPT EGNSVNLSCE TQLPPERSDT PLHFNFFRDG EV ILSDWST YPELQLPTVW RENSGSYWCG AETVRGNIHK HSPSLQIHVQ RIPVSGVLLE TQPSGGQAVE GEMLVLVCSV AEG TGDTTF SWHREDMQES LGRKTQRSLR AELELPAIRQ SHAGGYYCTA DNSYGPVQSM VLNVTVRETP GNRDGLHHHH HHHH HHSRV DYKDDDDK

UniProtKB: Interleukin-2, Fc receptor-like protein 4

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Macromolecule #2: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1

MacromoleculeName: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
type: protein_or_peptide / ID: 2 / 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

UniProtKB: Interleukin-2, Immunoglobulin heavy constant alpha 1

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Macromolecule #3: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.204727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MKNHLLFWGV LAVFIKAVHV KAQEDERIVL VDNKCKCARI TSRIIRSSED PNEDIVERNI RIIVPLNNRE NISDPTSPLR TRFVYHLSD LCKKCDPTEV ELDNQIVTAT QSNICDEDSA TETCYTYDRN KCYTAVVPLV YGGETKMVET ALTPDACYPD Y PYDVPDYA

UniProtKB: Immunoglobulin J chain

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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

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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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 300998
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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