+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6bbq | ||||||
---|---|---|---|---|---|---|---|
タイトル | Model for extended volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A Arf6 Q67L fusion protein | ||||||
要素 | Cytohesin-3,ADP-ribosylation factor 6 | ||||||
キーワード | LIPID BINDING PROTEIN / Guanine nucleotide exchange factor / Arf GTPase / Fusion protein / Inositol 1 / 3 / 4 / 5-tetrakisphosphate | ||||||
機能・相同性 | 機能・相同性情報 erythrocyte apoptotic process / Intra-Golgi traffic / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface ...erythrocyte apoptotic process / Intra-Golgi traffic / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / regulation of ARF protein signal transduction / endocytic recycling / MET receptor recycling / thioesterase binding / filopodium membrane / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / synaptic vesicle endocytosis / regulation of presynapse assembly / endocytic vesicle / positive regulation of cell adhesion / bicellular tight junction / signaling adaptor activity / vesicle-mediated transport / ruffle / positive regulation of protein localization to plasma membrane / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / guanyl-nucleotide exchange factor activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / adherens junction / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / Clathrin-mediated endocytosis / early endosome membrane / presynapse / nervous system development / cell cortex / midbody / postsynapse / endosome / cell differentiation / cell adhesion / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 35 Å | ||||||
データ登録者 | Das, S. / Malaby, A.W. / Lambright, D.G. | ||||||
資金援助 | 米国, 1件
| ||||||
引用 | ジャーナル: Structure / 年: 2018 タイトル: Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. 著者: Andrew W Malaby / Sanchaita Das / Srinivas Chakravarthy / Thomas C Irving / Osman Bilsel / David G Lambright / 要旨: Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and ...Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | 6bbq.cif.gz | 107.1 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6bbq.ent.gz | 76.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6bbq.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 | 6bbq_validation.pdf.gz | 775.6 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6bbq_full_validation.pdf.gz | 779.4 KB | 表示 | |
XML形式データ | 6bbq_validation.xml.gz | 19.2 KB | 表示 | |
CIF形式データ | 6bbq_validation.cif.gz | 28.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/bb/6bbq ftp://data.pdbj.org/pub/pdb/validation_reports/bb/6bbq | HTTPS FTP |
-関連構造データ
関連構造データ | 7078MC 7077C 6bbpC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
---|---|
類似構造データ | |
その他のデータベース |
|
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
#1: タンパク質 | 分子量: 60307.855 Da / 分子数: 1 / 変異: E161A,E161A / 由来タイプ: 組換発現 由来: (組換発現) Mus musculus (ハツカネズミ), (組換発現) Homo sapiens (ヒト) 遺伝子: Cyth3, Grp1, Pscd3, ARF6 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O08967, UniProt: P62330 |
---|---|
#2: 化合物 | ChemComp-GTP / |
#3: 化合物 | ChemComp-MG / |
#4: 化合物 | ChemComp-4IP / |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT |
---|---|
由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 8 詳細: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO |
染色 | タイプ: NEGATIVE / 詳細: Stained with 0.75% (w/v) uranyl formate / 染色剤: Uranyl Formate |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI TECNAI 12 詳細: Gatan Erlang Shen 785 camera used for collecting images |
---|---|
電子銃 | 電子線源: LAB6 / 加速電圧: 120 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 60000 X / 最大 デフォーカス(公称値): 3200 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2 mm |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: OTHER / 撮影したグリッド数: 1 / 実像数: 369 詳細: Gatan Erlang Shen 785 camera used for collecting images |
-解析
EMソフトウェア |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
画像処理 | 詳細: The images were X-ray corrected | ||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
粒子像の選択 | 選択した粒子像数: 10000 / 詳細: EMAN2 based manual particle picking | ||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||
3次元再構成 | 解像度: 35 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 6504 / クラス平均像の数: 71 / 対称性のタイプ: POINT |