+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2nsu | ||||||
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タイトル | Crystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex | ||||||
要素 | Transferrin receptor protein 1 | ||||||
キーワード | METAL TRANSPORT / transferrin receptor / virus-receptor complex | ||||||
機能・相同性 | 機能・相同性情報 transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / transport across blood-brain barrier / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / osteoclast differentiation / response to nutrient / acute-phase response / cellular response to leukemia inhibitory factor / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / Clathrin-mediated endocytosis / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / blood microparticle / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / 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 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 27 Å | ||||||
データ登録者 | Hafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G. | ||||||
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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Remark 999 | SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE ... SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE DIFFERENCES EXIST IN THE STRUCTURE 1CX8. THE UNIPROT ENTRY P02786 IS A RESULT OF DNA SEQUENCING, WHILE 1CX8 SEQUENCE IS APPARENTLY BASED ON MRNA SEQUENCE. |
-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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 2nsu.cif.gz | 252.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2nsu.ent.gz | 203 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2nsu.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 2nsu_validation.pdf.gz | 740.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2nsu_full_validation.pdf.gz | 827.5 KB | 表示 | |
XML形式データ | 2nsu_validation.xml.gz | 49 KB | 表示 | |
CIF形式データ | 2nsu_validation.cif.gz | 72.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ns/2nsu ftp://data.pdbj.org/pub/pdb/validation_reports/ns/2nsu | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 71622.961 Da / 分子数: 2 / 断片: THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TFRC / プラスミド: PCMVTFR / 器官 (発現宿主): OVARY CELLS 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P02786 |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS タイプ: VIRUS / 詳細: Based on PDB entry 1CX8 |
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緩衝液 | 名称: 0.02M TRIS-HCL / pH: 7.5 / 詳細: 0.02M TRIS-HCL |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: QUANTIFOIL 200 |
急速凍結 | 凍結剤: ETHANE / 詳細: PLUNGED IN LIQUID ETHANE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM200FEG / 日付: 2003年1月22日 |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 倍率(補正後): 54000 X / 最大 デフォーカス(公称値): 3900 nm / 最小 デフォーカス(公称値): 1700 nm / Cs: 2 mm |
撮影 | 電子線照射量: 25.96 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
画像スキャン | デジタル画像の数: 115 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: CTF correction of each particle | ||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||
3次元再構成 | 手法: projection matching / 解像度: 27 Å / 粒子像の数: 8566 / ピクセルサイズ(公称値): 2.6 Å / ピクセルサイズ(実測値): 2.6 Å / 詳細: a modified version of XMIPP software was used / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: BEST VISUAL FIT USING THE PROGRAM O 詳細: METHOD--MANUAL FITTING USING THE PROGRAM O REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
原子モデル構築 | PDB-ID: 1CX8 Accession code: 1CX8 / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 最高解像度: 27 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 27 Å
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