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- PDB-7t5m: Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex -

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基本情報

登録情報
データベース: PDB / ID: 7t5m
タイトルStructure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex
要素
  • Beta-2-microglobulin
  • Interleukin-27 receptor subunit alpha
  • MHC class I antigen
キーワードIMMUNE SYSTEM / HLA / long epitope / 20mer / T cell recognition
機能・相同性
機能・相同性情報


negative regulation of T cell extravasation / negative regulation of T-helper 17 type immune response / interleukin-27 receptor activity / negative regulation of type 2 immune response / regulation of isotype switching to IgG isotypes / positive regulation of T-helper 1 type immune response / negative regulation of interleukin-17 production / Interleukin-35 Signalling / Interleukin-27 signaling / cytokine binding ...negative regulation of T cell extravasation / negative regulation of T-helper 17 type immune response / interleukin-27 receptor activity / negative regulation of type 2 immune response / regulation of isotype switching to IgG isotypes / positive regulation of T-helper 1 type immune response / negative regulation of interleukin-17 production / Interleukin-35 Signalling / Interleukin-27 signaling / cytokine binding / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / cytokine-mediated signaling pathway / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / transmembrane signaling receptor activity / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane
類似検索 - 分子機能
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Fibronectin type III domain / MHC class I alpha chain, alpha1 alpha2 domains / Fibronectin type 3 domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Fibronectin type-III domain profile. / Beta-2-Microglobulin / Fibronectin type III / MHC class I-like antigen recognition-like ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Fibronectin type III domain / MHC class I alpha chain, alpha1 alpha2 domains / Fibronectin type 3 domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Fibronectin type-III domain profile. / Beta-2-Microglobulin / Fibronectin type III / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Fibronectin type III superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Beta-2-microglobulin / Interleukin-27 receptor subunit alpha / MHC class I antigen
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.67 Å
データ登録者Gras, S.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)1159272 オーストラリア
引用ジャーナル: J Immunol. / 年: 2022
タイトル: Cutting Edge: Unconventional CD8 + T Cell Recognition of a Naturally Occurring HLA-A*02:01-Restricted 20mer Epitope.
著者: Meeuwsen, M.H. / Wouters, A.K. / Hagedoorn, R.S. / Kester, M.G.D. / Remst, D.F.G. / van der Steen, D.M. / de Ru, A. / van Veelen, P.A. / Rossjohn, J. / Gras, S. / Falkenburg, J.H.F. / Heemskerk, M.H.M.
履歴
登録2021年12月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年12月14日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年1月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: Interleukin-27 receptor subunit alpha
F: Interleukin-27 receptor subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)92,2099
ポリマ－92,0386
非ポリマー1713
水21,9421218
1
A: MHC class I antigen
B: Beta-2-microglobulin
E: Interleukin-27 receptor subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,1665
ポリマ－46,0193
非ポリマー1462
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-26 kcal/mol
Surface area19440 Å2
手法PISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
F: Interleukin-27 receptor subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,0434
ポリマ－46,0193
非ポリマー241
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-31 kcal/mol
Surface area19280 Å2
手法PISA
単位格子
Length a, b, c (Å)70.178, 99.903, 135.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 MHC class I antigen


分子量: 32125.473 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q861F7
#2: タンパク質 Beta-2-microglobulin


分子量: 11748.160 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769

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タンパク質・ペプチド , 1種, 2分子 EF

#3: タンパク質・ペプチド Interleukin-27 receptor subunit alpha / IL-27 receptor subunit alpha / IL-27R subunit alpha / IL-27R-alpha / IL-27RA / Cytokine receptor ...IL-27 receptor subunit alpha / IL-27R subunit alpha / IL-27R-alpha / IL-27RA / Cytokine receptor WSX-1 / Cytokine receptor-like 1 / Type I T-cell cytokine receptor / TCCR / ZcytoR1


分子量: 2145.518 Da / 分子数: 2 / Fragment: residues 617-636 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q6UWB1

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非ポリマー , 3種, 1221分子

#4: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#5: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1218 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.58 Å3/Da /