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基本情報
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タイトル | Cryo-EM structure of human invariant chain in complex with HLA-DQ | |||||||||
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![]() | Antigen presentation / membrane protein / trimeric complex / IMMUNE SYSTEM | |||||||||
機能・相同性 | ![]() 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 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.12 Å | |||||||||
![]() | Wang N / Caveney NA / Jude KM / Garcia KC | |||||||||
資金援助 | ![]()
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![]() | ![]() 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. | |||||||||
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構造の表示
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 45.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 17.3 KB 17.3 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 7.9 KB | 表示 | ![]() |
画像 | ![]() | 148.2 KB | ||
マスクデータ | ![]() | 52.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
その他 | ![]() ![]() | 48.9 MB 48.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8vspMC ![]() 8vrwC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.2585 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_43501_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_43501_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : Trimeric complex of invariant chain associated with HLA-DQ alpha ...
全体 | 名称: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta |
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要素 |
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-超分子 #1: Trimeric complex of invariant chain associated with HLA-DQ alpha ...
超分子 | 名称: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 330 KDa |
-分子 #1: HLA class II histocompatibility antigen, DQ alpha 1 chain
分子 | 名称: HLA class II histocompatibility antigen, DQ alpha 1 chain タイプ: protein_or_peptide / ID: 1 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 31.599943 KDa |
組換発現 | 生物種: Mammalia (両生類) |
配列 | 文字列: MILNKALMLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ SYGPSGQYTH EFDGDEQFYV DLGRKETVWC LPVLRQFRFD PQFALTNIA VLKHNLNSLI KRSNSTAATN EVPEVTVFSK SPVTLGQPNI LICLVDNIFP PVVNITWLSN GHSVTEGVSE T SFLSKSDH ...文字列: MILNKALMLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ SYGPSGQYTH EFDGDEQFYV DLGRKETVWC LPVLRQFRFD PQFALTNIA VLKHNLNSLI KRSNSTAATN EVPEVTVFSK SPVTLGQPNI LICLVDNIFP PVVNITWLSN GHSVTEGVSE T SFLSKSDH SFFKISYLTL LPSAEESYDC KVEHWGLDKP LLKHWEPEIP APMSELTETV VCALGLSVGL VGIVVGTVFI IR GLRSVGA SRHQGPLAAA LEVLFQGPGA AEDQVDPRLI DGKHHHHHHH H UniProtKB: HLA class II histocompatibility antigen, DQ alpha 1 chain |
-分子 #2: HLA class II histocompatibility antigen, DQ beta 1 chain
分子 | 名称: HLA class II histocompatibility antigen, DQ beta 1 chain タイプ: protein_or_peptide / ID: 2 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 33.798309 KDa |
組換発現 | 生物種: Mammalia (両生類) |
配列 | 文字列: MSWKKALRIP GGLRAATVTL MLAMLSTPVA EGRDSPEDFV YQFKAMCYFT NGTERVRYVT RYIYNREEYA RFDSDVEVYR AVTPLGPPD AEYWNSQKEV LERTRAELDT VCRHNYQLEL RTTLQRRVEP TVTISPSRTE ALNHHNLLVC SVTDFYPAQI K VRWFRNDQ ...文字列: MSWKKALRIP GGLRAATVTL MLAMLSTPVA EGRDSPEDFV YQFKAMCYFT NGTERVRYVT RYIYNREEYA RFDSDVEVYR AVTPLGPPD AEYWNSQKEV LERTRAELDT VCRHNYQLEL RTTLQRRVEP TVTISPSRTE ALNHHNLLVC SVTDFYPAQI K VRWFRNDQ EETTGVVSTP LIRNGDWTFQ ILVMLEMTPQ HGDVYTCHVE HPSLQNPITV EWRAQSESAQ SKMLSGIGGF VL GLIFLGL GLIIHHRSQK GLLHAAALEV LFQGPGAAED QVDPRLIDGK HHHHHHHH UniProtKB: HLA class II histocompatibility antigen, DQ beta 1 chain |
-分子 #3: HLA class II histocompatibility antigen gamma chain
分子 | 名称: HLA class II histocompatibility antigen gamma chain / タイプ: protein_or_peptide / ID: 3 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 34.901906 KDa |
組換発現 | 生物種: Mammalia (両生類) |
配列 | 文字列: MDYKDDDDAG TSRHRRRSRS CREDQKPVMD DQRDLISNNE QLPMLGRRPG APESKCSRGA LYTGFSILVT LLLAGQATTA YFLYQQQGR LDKLTVTSQN LQLENLRMKL PKPPKPVSKM RMATPLLMQA LPMGALPQGP MQNATKYGNM TEDHVMHLLQ N ADPLKVYP ...文字列: MDYKDDDDAG TSRHRRRSRS CREDQKPVMD DQRDLISNNE QLPMLGRRPG APESKCSRGA LYTGFSILVT LLLAGQATTA YFLYQQQGR LDKLTVTSQN LQLENLRMKL PKPPKPVSKM RMATPLLMQA LPMGALPQGP MQNATKYGNM TEDHVMHLLQ N ADPLKVYP PLKGSFPENL RHLKNTMETI DWKVFESWMH HWLLFEMSRH SLEQKPTDAP PKVLTKCQEE VSHIPAVHPG SF RPKCDEN GNYLPLQCYG SIGYCWCVFP NGTEVPNTRS RGHHNCSESL ELEDPSSGLG VTKQDLGPVP M UniProtKB: HLA class II histocompatibility antigen gamma chain |
-分子 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 4 / コピー数: 3 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 5 mg/mL |
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緩衝液 | pH: 8 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 281 K / 装置: FEI VITROBOT MARK IV |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
精密化 | プロトコル: AB INITIO MODEL |
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得られたモデル | ![]() PDB-8vsp: |