[English] 日本語
Yorodumi
- PDB-9mbz: Cryo-EM structure of human FcRL4 bound to IgA-Fc/J -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mbz
TitleCryo-EM structure of human FcRL4 bound to IgA-Fc/J
Components
  • Immunoglobulin J chain
  • Interleukin-2,Fc receptor-like protein 4
  • Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
KeywordsIMMUNE SYSTEM / Immunoglobulin A / Fc receptor / FCRL4 / J-chain
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang, Y.X. / Su, C. / Xiao, J.Y.
Funding support China, 1items
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, Y.X. / Su, C. / Xiao, J.Y.
History
DepositionMar 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Interleukin-2,Fc receptor-like protein 4
A: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
B: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
C: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
D: Interleukin-2,Isoform 1 of Immunoglobulin heavy constant alpha 1
J: Immunoglobulin J chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,72012
Polymers192,0436
Non-polymers1,6776
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Interleukin-2,Fc receptor-like protein 4 / IL-2 / T-cell growth factor / TCGF / FcR-like protein 4 / FcRL4 / Fc receptor homolog 4 / FcRH4 / ...IL-2 / T-cell growth factor / TCGF / FcR-like protein 4 / FcRL4 / Fc receptor homolog 4 / FcRH4 / IFGP family protein 2 / hIFGP2 / Immune receptor translocation-associated protein 1


Mass: 47055.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2, FCRL4, FCRH4, IFGP2, IRTA1 / Production host: Homo sapiens (human) / References: UniProt: P60568, UniProt: Q96PJ5
#2: Protein
Interleukin-2,Isoform 1 of 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
#3: Protein Immunoglobulin J chain / Joining chain of multimeric IgA and IgM


Mass: 19204.727 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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ternary complex of IgA-Fc with the J-chain and FcRL4 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300998 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.019508
ELECTRON MICROSCOPYf_angle_d1.35212947
ELECTRON MICROSCOPYf_dihedral_angle_d5.5671298
ELECTRON MICROSCOPYf_chiral_restr0.0511529
ELECTRON MICROSCOPYf_plane_restr0.011630

+
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