IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / T=pseudo3 icosahedral viral capsid / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / host cell cytoplasmic vesicle membrane / 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 / cytoplasmic vesicle membrane / 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 / endocytosis involved in viral entry into host cell / 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 / 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 / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / protein complex oligomerization / late endosome membrane / monoatomic ion channel activity / iron ion transport / ER-Phagosome pathway / symbiont-mediated suppression of host gene expression / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / DNA replication / amyloid fibril formation / RNA helicase activity / learning or memory / endosome membrane / induction by virus of host autophagy / immune response / Amyloid fiber formation / RNA-directed RNA polymerase / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / Golgi membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity 類似検索 - 分子機能
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Class I Histocompatibility antigen, domains alpha 1 and 2 / Picornavirus/Calicivirus coat protein / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Viral coat protein subunit / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase 類似検索 - ドメイン・相同性
平均露光時間: 1.27 sec. / 電子線照射量: 54.48 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 実像数: 4531 / 詳細: Images were collected in movie-mode at 50 frames.
画像スキャン
サンプリングサイズ: 14 µm / 横: 4096 / 縦: 4096
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解析
ソフトウェア
名称: PHENIX / バージョン: (1.13_2992: ???) / 分類: 精密化
EMソフトウェア
ID
名称
バージョン
カテゴリ
1
RELION
3
粒子像選択
2
EPU
画像取得
13
RELION
3
3次元再構成
CTF補正
タイプ: PHASE FLIPPING ONLY
粒子像の選択
選択した粒子像数: 125031
対称性
点対称性: I (正20面体型対称)
3次元再構成
解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 13062 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT
原子モデル構築
手法: flexible fit / Target criteria: R-factors
精密化
解像度: 2.9→233.42 Å / SU ML: 0.65 / σ(F): 0.13 / 位相誤差: 34.06 / 立体化学のターゲット値: ML
Rfactor
反射数
%反射
Rfree
0.3108
36801
4.99 %
Rwork
0.3084
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obs
0.3085
738078
99.96 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL