+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8wyr | ||||||
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タイトル | Cryo-EM structure of human CD5L bound to IgM-Fc/J | ||||||
要素 |
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キーワード | IMMUNE SYSTEM / immunoglobulin / CD5 antigen-like / pentamer | ||||||
機能・相同性 | 機能・相同性情報 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 CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic 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 CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic 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 / negative regulation of T-helper 17 cell differentiation / IgA binding / positive regulation of tissue remodeling / pre-B cell allelic exclusion / glomerular filtration / IgM immunoglobulin complex / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / 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 / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / complement activation, classical pathway / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / negative regulation of protein phosphorylation / 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 / carbohydrate binding / positive regulation of cell growth / protein-containing complex assembly / 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 / serine-type endopeptidase activity / innate immune response / 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 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.39 Å | ||||||
データ登録者 | Wang, Y.X. / Su, C. / Xiao, J.Y. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2024 タイトル: CD5L associates with IgM via the J chain. 著者: Yuxin Wang / Chen Su / Chenggong Ji / Junyu Xiao / 要旨: 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. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8wyr.cif.gz | 481.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8wyr.ent.gz | 384.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8wyr.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8wyr_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8wyr_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 8wyr_validation.xml.gz | 83.1 KB | 表示 | |
CIF形式データ | 8wyr_validation.cif.gz | 120.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wy/8wyr ftp://data.pdbj.org/pub/pdb/validation_reports/wy/8wyr | HTTPS FTP |
-関連構造データ
関連構造データ | 37936MC 8wysC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 3種, 12分子 ABCDEFGHKLJM
#1: タンパク質 | 分子量: 44086.461 Da / 分子数: 10 / 由来タイプ: 組換発現 詳細: Signal peptide from Interleukin-2,Immunoglobulin heavy constant mu 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL2, IGHM / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P60568, UniProt: P01871 #2: タンパク質 | | 分子量: 19204.727 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: JCHAIN / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01591 #3: タンパク質 | | 分子量: 39757.547 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL2, CD5L, API6, UNQ203/PRO229 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P60568, UniProt: O43866 |
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-糖 , 2種, 11分子
#4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: 糖 | ChemComp-NAG / |
-非ポリマー , 1種, 2分子
#6: 化合物 |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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Has protein modification | Y |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Ternary complex of IgM-Fc with the J chain and CD5L / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: OTHER / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 1.5 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.39 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 381470 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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