+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6anu | ||||||||||||
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タイトル | Cryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain | ||||||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN (タンパク質) / actin binding protein / filament | ||||||||||||
機能・相同性 | 機能・相同性情報 cerebellar Purkinje cell layer morphogenesis / structural constituent of synapse / postsynaptic spectrin-associated cytoskeleton / structural constituent of postsynapse / regulation of postsynaptic specialization assembly / スペクトリン / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / paranodal junction / bBAF complex ...cerebellar Purkinje cell layer morphogenesis / structural constituent of synapse / postsynaptic spectrin-associated cytoskeleton / structural constituent of postsynapse / regulation of postsynaptic specialization assembly / スペクトリン / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / paranodal junction / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / regulation of transepithelial transport / morphogenesis of a polarized epithelium / Formation of annular gap junctions / GBAF complex / Gap junction degradation / dense body / regulation of G0 to G1 transition / postsynaptic actin cytoskeleton / Cell-extracellular matrix interactions / protein localization to adherens junction / Tat protein binding / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / Prefoldin mediated transfer of substrate to CCT/TriC / apical protein localization / actin filament capping / RHOF GTPase cycle / adherens junction assembly / Adherens junctions interactions / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / 密着結合 / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / parallel fiber to Purkinje cell synapse / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / maintenance of blood-brain barrier / adult behavior / establishment or maintenance of cell polarity / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / regulation of cyclin-dependent protein serine/threonine kinase activity / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / negative regulation of cell differentiation / 刷子縁 / kinesin binding / ヘルト萼状シナプス / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / COPI-mediated anterograde transport / regulation of protein localization to plasma membrane / vesicle-mediated transport / synapse assembly / EPHB-mediated forward signaling / substantia nigra development / MHC class II antigen presentation / NCAM signaling for neurite out-growth / 軸索誘導 / cell projection / 運動性 / RHO GTPases Activate Formins / マイクロフィラメント / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of protein binding / regulation of transmembrane transporter activity / positive regulation of cell differentiation / multicellular organism growth / FCGR3A-mediated phagocytosis / phospholipid binding / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / 接着結合 / DNA Damage Recognition in GG-NER / tau protein binding / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / 動原体 / Regulation of actin dynamics for phagocytic cup formation / 血小板 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / ネガティブ染色法 / クライオ電子顕微鏡法 / 解像度: 7 Å | ||||||||||||
データ登録者 | Wang, F. / Orlova, A. / Avery, A.W. / Hays, T.S. / Egelman, E.H. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2017 タイトル: Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation. 著者: Adam W Avery / Michael E Fealey / Fengbin Wang / Albina Orlova / Andrew R Thompson / David D Thomas / Thomas S Hays / Edward H Egelman / 要旨: Spinocerebellar ataxia type 5 (SCA5) is a neurodegenerative disease caused by mutations in the cytoskeletal protein β-III-spectrin. Previously, a SCA5 mutation resulting in a leucine-to-proline ...Spinocerebellar ataxia type 5 (SCA5) is a neurodegenerative disease caused by mutations in the cytoskeletal protein β-III-spectrin. Previously, a SCA5 mutation resulting in a leucine-to-proline substitution (L253P) in the actin-binding domain (ABD) was shown to cause a 1000-fold increase in actin-binding affinity. However, the structural basis for this increase is unknown. Here, we report a 6.9 Å cryo-EM structure of F-actin complexed with the L253P ABD. This structure, along with co-sedimentation and pulsed-EPR measurements, demonstrates that high-affinity binding caused by the CH2-localized mutation is due to opening of the two CH domains. This enables CH1 to bind actin aided by an unstructured N-terminal region that becomes α-helical upon binding. This helix is required for association with actin as truncation eliminates binding. Collectively, these results shed light on the mechanism by which β-III-spectrin, and likely similar actin-binding proteins, interact with actin, and how this mechanism can be perturbed to cause disease. | ||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6anu.cif.gz | 527.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6anu.ent.gz | 417.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6anu.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/an/6anu ftp://data.pdbj.org/pub/pdb/validation_reports/an/6anu | HTTPS FTP |
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-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 | らせん対称: (回転対称性: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 20 / Rise per n subunits: 27.25 Å / Rotation per n subunits: -166.87 °) |
詳細 | THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = -166.87 DEGREES RISE PER SUBUNIT (HEIGHT) = 27.25 ANGSTROMS |
-要素
#1: タンパク質 | 分子量: 41782.660 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACTB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P60709 #2: タンパク質 | 分子量: 32857.141 Da / 分子数: 6 / Mutation: L253P / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SPTBN2, KIAA0302, SCA5 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O15020 |
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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: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 | 名称: F-actin complexed with the spectrin actin-binding domain タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: YES |
染色 | タイプ: NEGATIVE / 染色剤: negative stain |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 平均露光時間: 3 sec. / 電子線照射量: 20 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 詳細: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the ...詳細: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2). |
画像スキャン | 動画フレーム数/画像: 7 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: dev_2471: / 分類: 精密化 | ||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: -166.87 ° / 軸方向距離/サブユニット: 27.25 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 7 Å / 解像度の算出法: OTHER / 粒子像の数: 12443 / アルゴリズム: BACK PROJECTION / 詳細: model-map FSC 0.38 cut-off / 対称性のタイプ: HELICAL | ||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||||||||||||
拘束条件 |
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