+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7use | ||||||
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タイトル | Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site | ||||||
要素 |
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キーワード | CELL INVASION / actin regulator / GTPase binding protein / cytoskeletal regulator | ||||||
機能・相同性 | 機能・相同性情報 peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone / modification of postsynaptic actin cytoskeleton / regulation of respiratory burst / dendrite extension / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / regulation of translation at postsynapse, modulating synaptic transmission / Activated NTRK2 signals through CDK5 / filopodium tip / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / WNT5:FZD7-mediated leishmania damping / respiratory burst / regulation of modification of postsynaptic actin cytoskeleton / regulation of actin filament polymerization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / RNA 7-methylguanosine cap binding / ruffle organization / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / cell projection assembly / RHO GTPases activate CIT / axon extension / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / motor neuron axon guidance / positive regulation of ruffle assembly / regulation of lamellipodium assembly / positive regulation of dendrite development / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / regulation of myelination / protein kinase A binding / lamellipodium assembly / cortical actin cytoskeleton organization / regulation of cell size / establishment or maintenance of cell polarity / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / positive regulation of actin filament polymerization / NRAGE signals death through JNK / Rac protein signal transduction / protein kinase A regulatory subunit binding / dendritic growth cone / filamentous actin / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / lamellipodium membrane / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / excitatory synapse / RHOG GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / localization / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / positive regulation of axon extension / axonal growth cone / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / signaling adaptor activity / response to electrical stimulus / positive regulation of substrate adhesion-dependent cell spreading 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: 3 Å | ||||||
データ登録者 | Ding, B. / Yang, S. / Chen, B. / Chowdhury, S. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Structures reveal a key mechanism of WAVE regulatory complex activation by Rac1 GTPase. 著者: Bojian Ding / Sheng Yang / Matthias Schaks / Yijun Liu / Abbigale J Brown / Klemens Rottner / Saikat Chowdhury / Baoyu Chen / 要旨: The Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites-the ...The Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites-the A and D sites. Precisely how Rac1 binds and how the binding triggers WRC activation remain unknown. Here we report WRC structures by itself, and when bound to single or double Rac1 molecules, at ~3 Å resolutions by cryogenic-electron microscopy. The structures reveal that Rac1 binds to the two sites by distinct mechanisms, and binding to the A site, but not the D site, drives WRC activation. Activation involves a series of unique conformational changes leading to the release of sequestered WCA (WH2-central-acidic) polypeptide, which stimulates the Arp2/3 complex to polymerize actin. Together with biochemical and cellular analyses, the structures provide a novel mechanistic understanding of how the Rac1-WRC-Arp2/3-actin signaling axis is regulated in diverse biological processes and diseases. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7use.cif.gz | 539.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7use.ent.gz | 429.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7use.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 | 7use_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7use_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 7use_validation.xml.gz | 83.2 KB | 表示 | |
CIF形式データ | 7use_validation.cif.gz | 127.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/us/7use ftp://data.pdbj.org/pub/pdb/validation_reports/us/7use | HTTPS FTP |
-関連構造データ
関連構造データ | 26734MC 7uscC 7usdC 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) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 5種, 5分子 ABCDE
#1: タンパク質 | 分子量: 145363.750 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map ...詳細: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CYFIP1, KIAA0068 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q7L576 |
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#2: タンパク質 | 分子量: 128940.727 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map ...詳細: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NCKAP1, HEM2, KIAA0587, NAP1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9Y2A7 |
#3: タンパク質 | 分子量: 37009.406 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Residues 231-248 are inserted as a flexible linker sequence. This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification ...詳細: Residues 231-248 are inserted as a flexible linker sequence. This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: WASF1, KIAA0269, SCAR1, WAVE1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q92558 |
#4: タンパク質 | 分子量: 8756.915 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: This construct contains uncleaved residues "GHMGAA" in the N terminus from the construct design and purification procedure. Densities for the residues are not observed in the map and were not ...詳細: This construct contains uncleaved residues "GHMGAA" in the N terminus from the construct design and purification procedure. Densities for the residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BRK1, C3orf10, HSPC300, MDS027 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8WUW1 |
#5: タンパク質 | 分子量: 18041.482 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: The sequence only contains residues 1-158. Also, there are two additional uncleaved residues "GH" in the N terminus from the construct design and purification procedure. Densities for these ...詳細: The sequence only contains residues 1-158. Also, there are two additional uncleaved residues "GH" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ABI2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: E9PEZ7 |
-Ras-related C3 botulinum toxin substrate ... , 2種, 2分子 FG
#6: タンパク質 | 分子量: 21025.459 Da / 分子数: 1 / Mutation: P29S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAC1, TC25, MIG5 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P63000, small monomeric GTPase |
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#7: タンパク質 | 分子量: 21010.486 Da / 分子数: 1 / Mutation: P29S, Q61L / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAC1, TC25, MIG5 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P63000, small monomeric GTPase |
-非ポリマー , 3種, 4分子
#8: 化合物 | ChemComp-GNP / | ||
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#9: 化合物 | #10: 化合物 | ChemComp-GTP / | |
-詳細
研究の焦点であるリガンドがあるか | 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: WAVE regulatory complex with Rac1 bound to A and D sites タイプ: COMPLEX / Entity ID: #1-#7 / 由来: MULTIPLE SOURCES | ||||||||||||
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分子量 | 値: 0.38 MDa / 実験値: NO | ||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | ||||||||||||
由来(組換発現) |
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緩衝液 | pH: 7 | ||||||||||||
試料 | 濃度: 0.15 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||
試料支持 | 詳細: 15 mA / グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: UltrAuFoil R1.2/1.3 | ||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 277.15 K |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TALOS ARCTICA 詳細: Data were collected by shifting the stage to target exposure positions. |
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): 120000 X / 最大 デフォーカス(公称値): 1200 nm / 最小 デフォーカス(公称値): 800 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: BASIC |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 40 sec. / 電子線照射量: 41.34 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 撮影したグリッド数: 1 / 実像数: 1285 詳細: Each micrograph was acquired as dose-fractionated movies consisting of 62 frames per movie. |
画像スキャン | サンプリングサイズ: 14 µm / 横: 4096 / 縦: 4096 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Particles were CTF-corrected during projection matching and back projection タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 666417 | ||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 139296 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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