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基本情報
登録情報 | データベース: EMDB / ID: EMD-8886 | ||||||||||||
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タイトル | Cryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain | ||||||||||||
![]() | Cryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain | ||||||||||||
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![]() | actin binding protein / filament / STRUCTURAL PROTEIN | ||||||||||||
機能・相同性 | ![]() cerebellar Purkinje cell layer morphogenesis / structural constituent of synapse / postsynaptic spectrin-associated cytoskeleton / structural constituent of postsynapse / spectrin / positive regulation of norepinephrine uptake / paranodal junction / regulation of postsynaptic specialization assembly / cellular response to cytochalasin B / bBAF complex ...cerebellar Purkinje cell layer morphogenesis / structural constituent of synapse / postsynaptic spectrin-associated cytoskeleton / structural constituent of postsynapse / spectrin / positive regulation of norepinephrine uptake / paranodal junction / regulation of postsynaptic specialization assembly / cellular response to cytochalasin B / bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / protein localization to adherens junction / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / dense body / Cell-extracellular matrix interactions / postsynaptic actin cytoskeleton / actin filament capping / Tat protein binding / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / apical protein localization / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / Sensory processing of sound by outer hair cells of the cochlea / tight junction / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / apical junction complex / maintenance of blood-brain barrier / transporter regulator activity / cortical actin cytoskeleton / positive regulation of double-strand break repair / parallel fiber to Purkinje cell synapse / nitric-oxide synthase binding / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / adult behavior / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / synapse assembly / vesicle-mediated transport / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / NCAM signaling for neurite out-growth / axonogenesis / MHC class II antigen presentation / calyx of Held / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / actin filament / adherens junction / positive regulation of cell differentiation / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / phospholipid binding / B-WICH complex positively regulates rRNA expression / kinetochore / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / 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 / tau protein binding / platelet aggregation / Schaffer collateral - CA1 synapse 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 7.0 Å | ||||||||||||
![]() | Wang F / Orlova A | ||||||||||||
資金援助 | ![]()
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![]() | ![]() 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 |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 24.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 12.7 KB 12.7 KB | 表示 表示 | ![]() |
画像 | ![]() | 180.3 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 467.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 467.5 KB | 表示 | |
XML形式データ | ![]() | 6 KB | 表示 | |
CIF形式データ | ![]() | 6.7 KB | 表示 | |
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : F-actin complexed with the spectrin actin-binding domain
全体 | 名称: F-actin complexed with the spectrin actin-binding domain |
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要素 |
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-超分子 #1: F-actin complexed with the spectrin actin-binding domain
超分子 | 名称: F-actin complexed with the spectrin actin-binding domain タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: ![]() |
-分子 #1: Actin, cytoplasmic 1
分子 | 名称: Actin, cytoplasmic 1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 6 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 41.78266 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...文字列: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF UniProtKB: Actin, cytoplasmic 1 |
-分子 #2: Spectrin beta chain, non-erythrocytic 2
分子 | 名称: Spectrin beta chain, non-erythrocytic 2 / タイプ: protein_or_peptide / ID: 2 / コピー数: 6 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 32.857141 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MSSTLSPTDF DSLEIQGQYS DINNRWDLPD SDWDNDSSSA RLFERSRIKA LADEREAVQK KTFTKWVNSH LARVTCRVGD LYSDLRDGR NLLRLLEVLS GEILPKPTKG RMRIHCLENV DKALQFLKEQ KVHLENMGSH DIVDGNHRLT LGLVWTIILR F QIQDISVE ...文字列: MSSTLSPTDF DSLEIQGQYS DINNRWDLPD SDWDNDSSSA RLFERSRIKA LADEREAVQK KTFTKWVNSH LARVTCRVGD LYSDLRDGR NLLRLLEVLS GEILPKPTKG RMRIHCLENV DKALQFLKEQ KVHLENMGSH DIVDGNHRLT LGLVWTIILR F QIQDISVE TEDNKEKKSA KDALLLWCQM KTAGYPNVNV HNFTTSWRDG LAFNAIVHKH RPDLLDFESL KKCNAHYNLQ NA FNLAEKE LGLTKPLDPE DVNVDQPDEK SIITYVATYY HYFSKMK UniProtKB: Spectrin beta chain, non-erythrocytic 2 |
-実験情報
-構造解析
手法 | ネガティブ染色法, クライオ電子顕微鏡法 |
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![]() | らせん対称体再構成法 |
試料の集合状態 | filament |
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試料調製
緩衝液 | pH: 7.4 |
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染色 | タイプ: NEGATIVE / 材質: negative stain |
凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / 平均露光時間: 3.0 sec. / 平均電子線量: 20.0 e/Å2 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). |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
最終 再構成 | 想定した対称性 - らせんパラメータ - Δz: 27.25 Å 想定した対称性 - らせんパラメータ - ΔΦ: -166.87 ° 想定した対称性 - らせんパラメータ - 軸対称性: C1 (非対称) アルゴリズム: BACK PROJECTION / 解像度のタイプ: BY AUTHOR / 解像度: 7.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: SPIDER / 詳細: model-map FSC 0.38 cut-off / 使用した粒子像数: 12443 |
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初期モデル | モデルのタイプ: OTHER / 詳細: low resolution pure actin filament map |
最終 角度割当 | タイプ: NOT APPLICABLE / ソフトウェア - 名称: SPIDER |
-原子モデル構築 1
精密化 | 空間: REAL |
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得られたモデル | ![]() PDB-6anu: |