+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8vsp | ||||||
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タイトル | Cryo-EM structure of human invariant chain in complex with HLA-DQ | ||||||
要素 |
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キーワード | IMMUNE SYSTEM / Antigen presentation / membrane protein / trimeric complex | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / T cell activation involved in immune response / positive regulation of type 2 immune response / T cell selection / positive regulation of prostaglandin biosynthetic process / negative thymic T cell selection / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / cytokine receptor activity / vacuole / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / regulation of macrophage activation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nitric-oxide synthase binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / antigen processing and presentation / humoral immune response / chaperone cofactor-dependent protein refolding / Generation of second messenger molecules / PD-1 signaling / immunoglobulin mediated immune response / positive regulation of chemokine production / positive regulation of B cell proliferation / protein folding chaperone / MHC class II antigen presentation / multivesicular body / lysosomal lumen / trans-Golgi network membrane / negative regulation of cell migration / clathrin-coated endocytic vesicle membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / intracellular protein transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / positive regulation of fibroblast proliferation / MHC class II protein complex / positive regulation of interleukin-6 production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of peptidyl-tyrosine phosphorylation / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / late endosome / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / amyloid-beta binding / positive regulation of canonical NF-kappaB signal transduction / protein-containing complex assembly / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / protein stabilization / positive regulation of protein phosphorylation / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / cell surface / protein-containing complex / extracellular exosome / identical protein binding / membrane / nucleus 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: 3.12 Å | ||||||
データ登録者 | Wang, N. / Caveney, N.A. / Jude, K.M. / Garcia, K.C. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2024 タイトル: Structural insights into human MHC-II association with invariant chain. 著者: Nan Wang / Deepa Waghray / Nathanael A Caveney / Kevin M Jude / K Christopher Garcia / 要旨: The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II ...The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II associates with the invariant chain (Ii) during biosynthesis in the endoplasmic reticulum to prevent premature peptide loading and to serve as a scaffold for subsequent proteolytic processing into MHC-II-CLIP. Cryo-electron microscopy structures of full-length Human Leukocyte Antigen-DR (HLA-DR) and HLA-DQ complexes associated with Ii, resolved at 3.0 to 3.1 Å, elucidate the trimeric assembly of the HLA/Ii complex and define atomic-level interactions between HLA, Ii transmembrane domains, loop domains, and class II-associated invariant chain peptides (CLIP). Together with previous structures of MHC-II peptide loading intermediates DO and DM, our findings complete the structural path governing class II antigen presentation. | ||||||
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 | 8vsp.cif.gz | 316.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8vsp.ent.gz | 238.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8vsp.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vs/8vsp ftp://data.pdbj.org/pub/pdb/validation_reports/vs/8vsp | HTTPS FTP |
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-関連構造データ
関連構造データ | 43501MC 8vrwC 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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-要素
#1: タンパク質 | 分子量: 31599.943 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DQA1 / 発現宿主: Mammalia (両生類) / 参照: UniProt: P01909 #2: タンパク質 | 分子量: 33798.309 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DQB1, HLA-DQB / 発現宿主: Mammalia (両生類) / 参照: UniProt: P01920 #3: タンパク質 | 分子量: 34901.906 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CD74, DHLAG / 発現宿主: Mammalia (両生類) / 参照: UniProt: P04233 #4: 糖 | 研究の焦点であるリガンドがあるか | Y | |
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-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: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
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分子量 | 値: 0.33 MDa / 実験値: YES |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Mammalia (両生類) |
緩衝液 | pH: 8 |
試料 | 濃度: 5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 281 K |
-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: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 60 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 3.12 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 421582 / 対称性のタイプ: POINT |
原子モデル構築 | プロトコル: AB INITIO MODEL |