+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1suv | ||||||
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タイトル | Structure of Human Transferrin Receptor-Transferrin Complex | ||||||
要素 |
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キーワード | METAL TRANSPORT / Protein Complex | ||||||
機能・相同性 | 機能・相同性情報 transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of cell motility / response to iron ion / response to copper ion / RND1 GTPase cycle / RND2 GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / endocytic vesicle / RHOH GTPase cycle / transport across blood-brain barrier / 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 / positive regulation of phosphorylation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / ERK1 and ERK2 cascade / osteoclast differentiation / ferric iron binding / response to nutrient / basal plasma membrane / cellular response to leukemia inhibitory factor / actin filament organization / acute-phase response / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of receptor-mediated endocytosis / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / recycling endosome membrane / double-stranded RNA binding / late endosome / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / antibacterial humoral response / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / apical plasma membrane / endoplasmic reticulum lumen / 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 / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / cell surface 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: 7.5 Å | ||||||
データ登録者 | Cheng, Y. / Zak, O. / Aisen, P. / Harrison, S.C. / Walz, T. | ||||||
引用 | ジャーナル: Cell / 年: 2004 タイトル: Structure of the human transferrin receptor-transferrin complex. 著者: Yifan Cheng / Olga Zak / Philip Aisen / Stephen C Harrison / Thomas Walz / 要旨: Iron, insoluble as free Fe(3+) and toxic as free Fe(2+), is distributed through the body as Fe(3+) bound to transferrin (Tf) for delivery to cells by endocytosis of its complex with transferrin ...Iron, insoluble as free Fe(3+) and toxic as free Fe(2+), is distributed through the body as Fe(3+) bound to transferrin (Tf) for delivery to cells by endocytosis of its complex with transferrin receptor (TfR). Although much is understood of the transferrin endocytotic cycle, little has been uncovered of the molecular details underlying the formation of the receptor-transferrin complex. Using cryo-electron microscopy, we have produced a density map of the TfR-Tf complex at subnanometer resolution. An atomic model, obtained by fitting crystal structures of diferric Tf and the receptor ectodomain into the map, shows that the Tf N-lobe is sandwiched between the membrane and the TfR ectodomain and that the C-lobe abuts the receptor helical domain. When Tf binds receptor, its N-lobe moves by about 9 A with respect to its C-lobe. The structure of TfR-Tf complex helps account for known differences in the iron-release properties of free and receptor bound Tf. | ||||||
履歴 |
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Remark 999 | SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 ...SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 A STRUCTURE OF THE TFR-TF COMPLEX WERE ALL HUMAN. THE AUTHORS CREATED THE MODEL BY FITTING X-RAY CRYSTAL STRUCTURES INTO THEIR 7.5 A EM DENSITY MAP. SINCE THERE IS NO STRUCTURE FOR THE HUMAN TRANSFERRIN C-LOBE, THE AUTHORS OPTED TO USE THE C-LOBE FROM RABBIT TF (1JNF). THE OTHER TWO CHAINS ARE HUMAN (1CX8 - HUMAN TFR AND 1A8E - HUMAN TF N-LOBE). THE CHAINS E AND F MATCH SWS P19134, A RABBIT SOURCE. REGARDING THE CONFLICTS: BOTH SEQUENCE AND COORDINATES ARE FROM THE ORIGINAL PDB-FILES AND THE AUTHORS DID NOT MAKE ANY MODIFICATIONS TO IT. |
-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 | 1suv.cif.gz | 511.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1suv.ent.gz | 411.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1suv.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 | 1suv_validation.pdf.gz | 409.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1suv_full_validation.pdf.gz | 541.7 KB | 表示 | |
XML形式データ | 1suv_validation.xml.gz | 69.6 KB | 表示 | |
CIF形式データ | 1suv_validation.cif.gz | 98.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/su/1suv ftp://data.pdbj.org/pub/pdb/validation_reports/su/1suv | 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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対称性 | 点対称性: (シェーンフリース記号: C2 (2回回転対称)) |
-要素
#1: タンパク質 | 分子量: 71622.961 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: TFRC / Cell (発現宿主): ovary 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P02786 #2: タンパク質 | 分子量: 36408.414 Da / 分子数: 2 / Fragment: repeat 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TF / Cell (発現宿主): kidney 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P02787 #3: タンパク質 | 分子量: 38300.445 Da / 分子数: 2 / Fragment: repeat 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TF / Cell (発現宿主): kidney 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) #4: 化合物 | ChemComp-CO3 / #5: 化合物 | ChemComp-FE / Has protein modification | Y | |
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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: Human Transferrin Receptor - Transferrin Complex / タイプ: COMPLEX |
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緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 / 日付: 2001年10月15日 |
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): 51160 X / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 2500 nm / Cs: 2 mm |
試料ホルダ | 温度: 93 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
CTF補正 | 詳細: CTF correction for each particle | ||||||||||||||||||||||||||||
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対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||
3次元再構成 | 手法: Fourier Space reconstruction / 解像度: 7.5 Å / ピクセルサイズ(公称値): 2.8 Å / ピクセルサイズ(実測値): 2.74 Å / 詳細: using program FREALIGN / 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: visual fit using program O followed by rigid body refinement using program MAVE 詳細: REFINEMENT PROTOCOL--rigid body | ||||||||||||||||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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