+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-1288 | |||||||||
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タイトル | Asymmetric binding of transferrin receptor to parvovirus capsids. | |||||||||
マップデータ | Three-dimensional reconstruction of canine parvovirus with bound feline transferrin receptor. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to copper ion / response to iron ion / RND1 GTPase cycle / response to manganese ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to copper ion / response to iron ion / RND1 GTPase cycle / response to manganese ion / RND2 GTPase cycle / positive regulation of bone resorption / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / transport across blood-brain barrier / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / response to nutrient / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / osteoclast differentiation / clathrin-coated endocytic vesicle membrane / cellular response to leukemia inhibitory factor / acute-phase response / positive regulation of protein-containing complex assembly / HFE-transferrin receptor complex / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / cellular response to xenobiotic stimulus / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / double-stranded RNA binding / extracellular vesicle / Clathrin-mediated endocytosis / virus receptor activity / melanosome / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / iron ion transport / basolateral plasma membrane / cytoplasmic vesicle / intracellular iron ion homeostasis / blood microparticle / endosome / endosome membrane / early endosome / response to hypoxia / intracellular signal transduction / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Felis silvestris (ヨーロッパヤマネコ) / Canine parvovirus 2 (ウイルス) | |||||||||
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: 27.0 Å | |||||||||
データ登録者 | Hafenstein S / Palermo LM / Xiao C / Kostyuchenko VA / Morais M / Nelson CDS / Chipman PR / Bowman VD / Battisti AJ / Parrish CR / Rossmann MG | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2007 タイトル: Asymmetric binding of transferrin receptor to parvovirus capsids. 著者: Susan Hafenstein / Laura M Palermo / Victor A Kostyuchenko / Chuan Xiao / Marc C Morais / Christian D S Nelson / Valorie D Bowman / Anthony J Battisti / Paul R Chipman / Colin R Parrish / Michael G Rossmann / 要旨: Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry ...Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry and conformation of the original infecting virion in preparation for membrane penetration and release of the viral genome. Cryoelectron microscopy and biochemical analyses show that transferrin receptor, the cellular receptor for canine parvovirus, can bind to only one or a few of the 60 icosahedrally equivalent sites on the virion, indicating that either canine parvovirus has inherent asymmetry or binding of receptor induces asymmetry. The asymmetry of receptor binding to canine parvovirus is reminiscent of the special portal in tailed bacteriophages and some large, icosahedral viruses. Asymmetric interactions of icosahedral viruses with their hosts might be a more common phenomenon than previously thought and may have been obscured by averaging in previous crystallographic and electron microscopic structure determinations. | |||||||||
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_1288.map.gz | 48 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-1288-v30.xml emd-1288.xml | 11 KB 11 KB | 表示 表示 | EMDBヘッダ |
画像 | 1288.gif | 15.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-1288 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1288 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_1288_validation.pdf.gz | 297.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_1288_full_validation.pdf.gz | 297.4 KB | 表示 | |
XML形式データ | emd_1288_validation.xml.gz | 6.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1288 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1288 | 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_1288.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Three-dimensional reconstruction of canine parvovirus with bound feline transferrin receptor. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.6 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 : Canine parvovirus complexed with feline transferrin receptor
全体 | 名称: Canine parvovirus complexed with feline transferrin receptor |
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要素 |
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-超分子 #1000: Canine parvovirus complexed with feline transferrin receptor
超分子 | 名称: Canine parvovirus complexed with feline transferrin receptor タイプ: sample / ID: 1000 集合状態: one homodimer of fTfR binds to one icosahedral CPV particle Number unique components: 2 |
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-超分子 #1: Canine parvovirus 2
超分子 | 名称: Canine parvovirus 2 / タイプ: virus / ID: 1 / Name.synonym: CPV / 詳細: empty capsids / NCBI-ID: 246878 / 生物種: Canine parvovirus 2 / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: No / ウイルス・中空状態: Yes / Syn species name: CPV |
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宿主 | 生物種: Canis lupus (オオカミ) / 別称: VERTEBRATES |
ウイルス殻 | Shell ID: 1 / 名称: capsid / 直径: 280 Å / T番号(三角分割数): 1 |
-分子 #1: feline transferrin receptor
分子 | 名称: feline transferrin receptor / タイプ: protein_or_peptide / ID: 1 / Name.synonym: feTfR / 詳細: ectodomain only / コピー数: 2 / 集合状態: dimer / 組換発現: Yes |
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由来(天然) | 生物種: Felis silvestris (ヨーロッパヤマネコ) / 別称: Feline |
組換発現 | 生物種: unidentified baculovirus (ウイルス) / 組換プラスミド: pcDNA 3.1 |
-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 | particle |
-試料調製
緩衝液 | pH: 7.5 / 詳細: 20 mM Tris-HCl |
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染色 | タイプ: NEGATIVE / 詳細: no staining |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM200FEG |
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温度 | 平均: 100 K |
日付 | 2003年1月22日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: ZEISS SCAI / デジタル化 - サンプリング間隔: 14 µm / 実像数: 115 / 平均電子線量: 25.96 e/Å2 / ビット/ピクセル: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 54000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 3.9 µm / 最小 デフォーカス(公称値): 1.7 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダー: 626 Single Tilt Cryotransfer System / 試料ホルダーモデル: GATAN LIQUID NITROGEN |
-画像解析
CTF補正 | 詳細: CTF correction of each particle |
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最終 再構成 | 想定した対称性 - 点群: I (正20面体型対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 27.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: XMIPP with modifications 詳細: Intermediate reconstructions were made from images with virus density subtracted, final reconstruction was calculated from complete images. 使用した粒子像数: 8566 |
最終 角度割当 | 詳細: initial angles were selected using SPIDER VO EA procedure with limits for theta of 0-40, phi of 0-72 to cover an asymmetric unit of an icosahedron; During orientation search the angles were ...詳細: initial angles were selected using SPIDER VO EA procedure with limits for theta of 0-40, phi of 0-72 to cover an asymmetric unit of an icosahedron; During orientation search the angles were changed to be one of the 60 icosahedral symmetry equivalent triplet. |
最終 2次元分類 | クラス数: 226 |