+Open data
-Basic information
Entry | Database: PDB / ID: 8wyr | ||||||
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Title | Cryo-EM structure of human CD5L bound to IgM-Fc/J | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / CD5 antigen-like / pentamer | ||||||
Function / homology | Function and homology information positive regulation of complement-dependent cytotoxicity / hexameric IgM immunoglobulin complex / kappa-type opioid receptor binding / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex ...positive regulation of complement-dependent cytotoxicity / hexameric IgM immunoglobulin complex / kappa-type opioid receptor binding / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / IgA binding / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / pre-B cell allelic exclusion / IgM immunoglobulin complex / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / glomerular filtration / regulation of complement activation / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / natural killer cell activation / activated T cell proliferation / kinase activator activity / positive regulation of regulatory T cell differentiation / : / CD22 mediated BCR regulation / negative regulation of B cell apoptotic process / zymogen activation / Interleukin-2 signaling / positive regulation of immunoglobulin production / immune system process / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of respiratory burst / positive regulation of interleukin-17 production / immunoglobulin complex, circulating / immunoglobulin receptor binding / humoral immune response / T cell differentiation / Interleukin receptor SHC signaling / cellular defense response / Scavenging of heme from plasma / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of B cell proliferation / complement activation, classical pathway / antigen binding / negative regulation of protein phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 inflammatory response / positive regulation of type II interferon production / cell-cell signaling / antibacterial humoral response / protein-macromolecule adaptor activity / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / protein-containing complex assembly / carbohydrate binding / defense response to Gram-negative bacterium / response to ethanol / adaptive immune response / blood microparticle / transcription by RNA polymerase II / Potential therapeutics for SARS / cell adhesion / inflammatory response / immune response / innate immune response / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||
Authors | Wang, Y.X. / Su, C. / Xiao, J.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: CD5L associates with IgM via the J chain. Authors: Yuxin Wang / Chen Su / Chenggong Ji / Junyu Xiao / Abstract: CD5 antigen-like (CD5L), also known as Spα or AIM (Apoptosis inhibitor of macrophage), emerges as an integral component of serum immunoglobulin M (IgM). However, the molecular mechanism underlying ...CD5 antigen-like (CD5L), also known as Spα or AIM (Apoptosis inhibitor of macrophage), emerges as an integral component of serum immunoglobulin M (IgM). However, the molecular mechanism underlying the interaction between IgM and CD5L has remained elusive. In this study, we present a cryo-electron microscopy structure of the human IgM pentamer core in complex with CD5L. Our findings reveal that CD5L binds to the joining chain (J chain) in a Ca-dependent manner and further links to IgM via a disulfide bond. We further corroborate recently published data that CD5L reduces IgM binding to the mucosal transport receptor pIgR, but does not impact the binding of the IgM-specific receptor FcμR. Additionally, CD5L does not interfere with IgM-mediated complement activation. These results offer a more comprehensive understanding of IgM and shed light on the function of the J chain in the immune system. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wyr.cif.gz | 481.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wyr.ent.gz | 384.5 KB | Display | PDB format |
PDBx/mmJSON format | 8wyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wyr_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8wyr_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8wyr_validation.xml.gz | 83.1 KB | Display | |
Data in CIF | 8wyr_validation.cif.gz | 120.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/8wyr ftp://data.pdbj.org/pub/pdb/validation_reports/wy/8wyr | HTTPS FTP |
-Related structure data
Related structure data | 37936MC 8wysC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 12 molecules ABCDEFGHKLJM
#1: Protein | Mass: 44086.461 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Details: Signal peptide from Interleukin-2,Immunoglobulin heavy constant mu Source: (gene. exp.) Homo sapiens (human) / Gene: IL2, IGHM / Production host: Homo sapiens (human) / References: UniProt: P60568, UniProt: P01871 #2: Protein | | Mass: 19204.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JCHAIN / Production host: Homo sapiens (human) / References: UniProt: P01591 #3: Protein | | Mass: 39757.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2, CD5L, API6, UNQ203/PRO229 / Production host: Homo sapiens (human) / References: UniProt: P60568, UniProt: O43866 |
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-Sugars , 2 types, 11 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 2 molecules
#6: Chemical |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of IgM-Fc with the J chain and CD5L / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 381470 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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