+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9895 | |||||||||
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タイトル | Structure of human T cell receptor-CD3 complex | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / T cell activation involved in immune response / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / T cell activation involved in immune response / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / Fc-gamma receptor signaling pathway / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of protein localization to cell surface / signal complex assembly / Nef and signal transduction / positive regulation of cell-matrix adhesion / T cell receptor complex / establishment or maintenance of cell polarity / smoothened signaling pathway / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / FCGR activation / PD-1 signaling / Role of phospholipids in phagocytosis / T cell receptor binding / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / T cell activation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / FCGR3A-mediated IL10 synthesis / cerebellum development / protein tyrosine kinase binding / clathrin-coated endocytic vesicle membrane / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / response to bacterium / calcium-mediated signaling / transmembrane signaling receptor activity / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / positive regulation of type II interferon production / peptide antigen binding / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / protein transport / Downstream TCR signaling / protein complex oligomerization / T cell receptor signaling pathway / cell body / protein-containing complex assembly / regulation of apoptotic process / adaptive immune response / dendritic spine / cell surface receptor signaling pathway / protein heterodimerization activity / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 3.7 Å | |||||||||
データ登録者 | Dong D / Zheng L / Lin J / Zhu Y / Li N / Zhang B / Xie S / Zheng J / Wang Y / Gao N / Huang Z | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Structural basis of assembly of the human T cell receptor-CD3 complex. 著者: De Dong / Lvqin Zheng / Jianquan Lin / Bailing Zhang / Yuwei Zhu / Ningning Li / Shuangyu Xie / Yuhang Wang / Ning Gao / Zhiwei Huang / 要旨: The αβ T cell receptor (TCR), in association with the CD3γε-CD3δε-CD3ζζ signalling hexamer, is the primary determinant of T cell development and activation, and of immune responses to foreign ...The αβ T cell receptor (TCR), in association with the CD3γε-CD3δε-CD3ζζ signalling hexamer, is the primary determinant of T cell development and activation, and of immune responses to foreign antigens. The mechanism of assembly of the TCR-CD3 complex remains unknown. Here we report a cryo-electron microscopy structure of human TCRαβ in complex with the CD3 hexamer at 3.7 Å resolution. The structure contains the complete extracellular domains and all the transmembrane helices of TCR-CD3. The octameric TCR-CD3 complex is assembled with 1:1:1:1 stoichiometry of TCRαβ:CD3γε:CD3δε:CD3ζζ. Assembly of the extracellular domains of TCR-CD3 is mediated by the constant domains and connecting peptides of TCRαβ that pack against CD3γε-CD3δε, forming a trimer-like structure proximal to the plasma membrane. The transmembrane segment of the CD3 complex adopts a barrel-like structure formed by interaction of the two transmembrane helices of CD3ζζ with those of CD3γε and CD3δε. Insertion of the transmembrane helices of TCRαβ into the barrel-like structure via both hydrophobic and ionic interactions results in transmembrane assembly of the TCR-CD3 complex. Together, our data reveal the structural basis for TCR-CD3 complex assembly, providing clues to TCR triggering and a foundation for rational design of immunotherapies that target the complex. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_9895.map.gz | 78.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9895-v30.xml emd-9895.xml | 15.9 KB 15.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9895.png | 39.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9895 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9895_validation.pdf.gz | 444.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9895_full_validation.pdf.gz | 443.7 KB | 表示 | |
XML形式データ | emd_9895_validation.xml.gz | 6.1 KB | 表示 | |
CIF形式データ | emd_9895_validation.cif.gz | 6.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9895 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_9895.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.057 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : complex
全体 | 名称: complex |
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要素 |
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-超分子 #1: complex
超分子 | 名称: complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-分子 #1: T-cell surface glycoprotein CD3 zeta chain
分子 | 名称: T-cell surface glycoprotein CD3 zeta chain / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 18.723439 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MKWKALFTAA ILQAQLPITE AQSFGLLDPK LCYLLDGILF IYGVILTALF LRVKFSRSAD APAYQQGQNQ LYNELNLGRR EEYDVLDKR RGRDPEMGGK PQRRKNPQEG LYNELQKDKM AEAYSEIGMK GERRRGKGHD GLYQGLSTAT KDTYDALHMQ A LPPR |
-分子 #2: T-cell surface glycoprotein CD3 delta chain
分子 | 名称: T-cell surface glycoprotein CD3 delta chain / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 18.949537 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MEHSTFLSGL VLATLLSQVS PFKIPIEELE DRVFVNCNTS ITWVEGTVGT LLSDITRLDL GKRILDPRGI YRCNGTDIYK DKESTVQVH YRMCQSCVEL DPATVAGIIV TDVIATLLLA LGVFCFAGHE TGRLSGAADT QALLRNDQVY QPLRDRDDAQ Y SHLGGNWA RNK |
-分子 #3: T-cell surface glycoprotein CD3 epsilon chain
分子 | 名称: T-cell surface glycoprotein CD3 epsilon chain / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 23.174227 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA ...文字列: MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA GGRQRGQNKE RPPPVPNPDY EPIRKGQRDL YSGLNQRRI |
-分子 #4: T-cell surface glycoprotein CD3 gamma chain
分子 | 名称: T-cell surface glycoprotein CD3 gamma chain / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 20.493457 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MEQGKGLAVL ILAIILLQGT LAQSIKGNHL VKVYDYQEDG SVLLTCDAEA KNITWFKDGK MIGFLTEDKK KWNLGSNAKD PRGMYQCKG SQNKSKPLQV YYRMCQNCIE LNAATISGFL FAEIVSIFVL AVGVYFIAGQ DGVRQSRASD KQTLLPNDQL Y QPLKDRED DQYSHLQGNQ LRRN |
-分子 #5: T cell receptor alpha variable 12-3,Possible J 11 gene segment,T ...
分子 | 名称: T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constant タイプ: protein_or_peptide / ID: 5 詳細: fusion protein of residues 22-114 from A0A0B4J271, residues 116-132 from A0N4Z6 and residues 134-273 from P01848. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 28.308662 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: QQKEVEQDPG PLSVPEGAIV SLNCTYSNSA FQYFMWYRQY SRKGPELLMY TYSSGNKEDG RFTAQVDKSS KYISLFIRDS QPSDSATYL CAMSKGYSTL TFGKGTMLLV SPDIQNPDPA VYQLRDSKSS DKSVCLFTDF DSQTNVSQSK DSDVYITDKT V LDMRSMDF ...文字列: QQKEVEQDPG PLSVPEGAIV SLNCTYSNSA FQYFMWYRQY SRKGPELLMY TYSSGNKEDG RFTAQVDKSS KYISLFIRDS QPSDSATYL CAMSKGYSTL TFGKGTMLLV SPDIQNPDPA VYQLRDSKSS DKSVCLFTDF DSQTNVSQSK DSDVYITDKT V LDMRSMDF KSNSAVAWSN KSDFACANAF NNSIIPEDTF FPSPESSCDV KLVEKSFETD TNLNFQNLSV IGFRILLLKV AG FNLLMTL RLWSS |
-分子 #6: T cell receptor beta variable 6-5,M1-specific T cell receptor bet...
分子 | 名称: T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 タイプ: protein_or_peptide / ID: 6 詳細: fusion protein of residues 22-112 from A0A0K0K1A5, residues 121-134 from P0DSE2 and residues 135-312 from A0A0G2JMB4. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 32.498463 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: GVTQTPKFQV LKTGQSMTLQ CAQDMNHEYM SWYRQDPGMG LRLIHYSVGA GITDQGEVPN GYNVSRSTTE DFPLRLLSAA PSQTSVYFC ASRRRQGASG EQYFGPGTRL TVTEDLKNVF PPEVAVFEPS EAEISHTQKA TLVCLATGFY PDHVELSWWV N GKEVHSGV ...文字列: GVTQTPKFQV LKTGQSMTLQ CAQDMNHEYM SWYRQDPGMG LRLIHYSVGA GITDQGEVPN GYNVSRSTTE DFPLRLLSAA PSQTSVYFC ASRRRQGASG EQYFGPGTRL TVTEDLKNVF PPEVAVFEPS EAEISHTQKA TLVCLATGFY PDHVELSWWV N GKEVHSGV STDPQPLKEQ PALNDSRYCL SSRLRVSATF WQNPRNHFRC QVQFYGLSEN DEWTQDRAKP VTQIVSAEAW GR ADCGFTS ESYQQGVLSA TILYEILLGK ATLYAVLVSA LVLMAMVKRK DSRG |
-実験情報
-構造解析
手法 | ネガティブ染色法, クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | cell |
-試料調製
緩衝液 | pH: 7.5 |
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染色 | タイプ: NEGATIVE / 材質: Uranyl Acetate |
凍結 | 凍結剤: NITROGEN |
-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 K2 SUMMIT (4k x 4k) 平均電子線量: 64.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: DARK FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 197487 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |