- PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -
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基本情報
登録情報
データベース: PDB / ID: 2nsu
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 / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / response to iron ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / response to iron ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / 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 / response to nutrient / osteoclast differentiation / cellular response to leukemia inhibitory factor / acute-phase response / clathrin-coated endocytic vesicle membrane / positive regulation of protein-containing complex assembly / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / 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 / Clathrin-mediated endocytosis / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / early endosome / blood microparticle / endosome membrane / response to hypoxia / 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
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28 類似検索 - ドメイン・相同性
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.
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.
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
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解析
EMソフトウェア
ID
名称
カテゴリ
1
EMAN
3次元再構成
2
SPIDER
3次元再構成
3
Xmipp
3次元再構成
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