+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11869 | |||||||||
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タイトル | Structure of the actin filament Arp2/3 complex branch junction in cells | |||||||||
マップデータ | Structure of the actin filament Arp2/3 complex branch junction | |||||||||
試料 |
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キーワード | Actin / Arp2-3 complex / Cytoskeleton / STRUCTURAL PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization ...podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / peripheral region of growth cone / muscle cell projection membrane / : / meiotic cytokinesis / apical ectoplasmic specialization / basal ectoplasmic specialization / cellular response to rapamycin / lamellipodium organization / spindle localization / : / skeletal muscle fiber adaptation / leading edge of lamellipodium / Striated Muscle Contraction / EPHB-mediated forward signaling / cellular response to trichostatin A / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / hemidesmosome / asymmetric cell division / protein kinase C signaling / Arp2/3 complex-mediated actin nucleation / actin filament network formation / podosome ring / orbitofrontal cortex development / actin cap / postsynaptic actin cytoskeleton organization / Regulation of actin dynamics for phagocytic cup formation / negative regulation of axon extension / maintenance of cell polarity / Clathrin-mediated endocytosis / positive regulation of dendritic spine morphogenesis / positive regulation of astrocyte differentiation / : / apical dendrite / astrocyte differentiation / positive regulation of fibroblast migration / podosome / positive regulation of synapse assembly / positive regulation of podosome assembly / positive regulation of dendrite morphogenesis / response to steroid hormone / positive regulation of filopodium assembly / smooth muscle cell migration / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cellular response to platelet-derived growth factor stimulus / mesenchyme migration / positive regulation of smooth muscle cell migration / cell leading edge / filamentous actin / brush border / associative learning / skeletal muscle thin filament assembly / striated muscle thin filament / excitatory synapse / response to immobilization stress / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of protein targeting to membrane / glutamate receptor binding / skeletal muscle fiber development / positive regulation of lamellipodium assembly / stress fiber / response to mechanical stimulus / positive regulation of substrate adhesion-dependent cell spreading / axon terminus / cellular response to epidermal growth factor stimulus / cellular response to transforming growth factor beta stimulus / ruffle / cytoskeletal protein binding / positive regulation of neuron differentiation / actin filament polymerization / Neutrophil degranulation / cellular response to nerve growth factor stimulus / secretory granule / meiotic cell cycle / filopodium / dendritic shaft / cell projection / actin filament / positive regulation of protein localization to plasma membrane / 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 / structural constituent of cytoskeleton / cellular response to type II interferon / ruffle membrane / actin filament binding / cell-cell junction 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 9.0 Å | |||||||||
データ登録者 | Faessler F / Dimchev G | |||||||||
資金援助 | オーストリア, 1件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. 著者: Florian Fäßler / Georgi Dimchev / Victor-Valentin Hodirnau / William Wan / Florian K M Schur / 要旨: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves ...The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_11869.map.gz | 49.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11869-v30.xml emd-11869.xml | 36.7 KB 36.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11869_fsc.xml | 8.7 KB | 表示 | FSCデータファイル |
画像 | emd_11869.png | 39.9 KB | ||
マスクデータ | emd_11869_msk_1.map | 52.7 MB | マスクマップ | |
Filedesc metadata | emd-11869.cif.gz | 8.4 KB | ||
その他 | emd_11869_half_map_1.map.gz emd_11869_half_map_2.map.gz | 27 MB 27 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11869 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11869 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_11869.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Structure of the actin filament Arp2/3 complex branch junction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.137 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
-マスク #1
ファイル | emd_11869_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1
ファイル | emd_11869_half_map_1.map | ||||||||||||
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注釈 | Half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2
ファイル | emd_11869_half_map_2.map | ||||||||||||
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注釈 | Half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Actin Filament Arp2/3 Complex Branch Junction
全体 | 名称: Actin Filament Arp2/3 Complex Branch Junction |
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要素 |
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-超分子 #1: Actin Filament Arp2/3 Complex Branch Junction
超分子 | 名称: Actin Filament Arp2/3 Complex Branch Junction / タイプ: cell / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
-分子 #1: Actin-related protein 2, Arp2
分子 | 名称: Actin-related protein 2, Arp2 / タイプ: protein_or_peptide / ID: 1 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 44.818711 KDa |
配列 | 文字列: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP ...文字列: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP VYEGFSLPHL TRRLDIAGRD ITRYLIKLLL LRGYAFNHSA DFETVRMIKE KLCYVGYNIE QEQKLALETT VL VESYTLP DGRIIKVGGE RFEAPEALFQ PHLINVEGVG VAELLFNTIQ AADIDTRSEF YKHIVLSGGS TMYPGLPSRL ERE LKQLYL ERVLKGDVEK LSKFKIRIED PPRRKHMVFL GGAVLADIMK DKDNFWMTRQ EYQEKGVRVL EKLGVTVR |
-分子 #2: Actin-related protein 3, Arp3
分子 | 名称: Actin-related protein 3, Arp3 / タイプ: protein_or_peptide / ID: 2 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 47.428031 KDa |
配列 | 文字列: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI ...文字列: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI DSGDGVTHVI PVAEGYVIGS CIKHIPIAGR DITYFIQQLL RDREVGIPPE QSLETAKAVK ERYSYVCPDL VK EFNKYDT DGSKWIKQYT GINAISKKEF SIDVGYERFL GPEIFFHPEF ANPDFTQPIS EVVDEVIQNC PIDVRRPLYK NIV LSGGST MFRDFGRRLQ RDLKRTVDAR LKLSEELSGG RLKPKPIDVQ VITHHMQRYA VWFGGSMLAS TPEFYQVCHT KKDY EEIGP SICRHNPVFG VMS |
-分子 #3: Actin-related protein 2/3 complex subunit 1b, ArpC1b
分子 | 名称: Actin-related protein 2/3 complex subunit 1b, ArpC1b タイプ: protein_or_peptide / ID: 3 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 41.016738 KDa |
配列 | 文字列: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGVDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI ...文字列: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGVDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI FSAYIKEVEE RPAPTPWGSK MPFGELMFES SSSCGWVHGV CFSANGSRVA WVSHDSTVCL ADADKKMAVA TL ASETLPL LAVTFITESS LVAAGHDCFP VLFTYDSAAG KLSFGGRLDV PKQSSQRGLT ARERFQNLDK KASSEGSAAA GAG LDSLHK NSVSQISVLS GGKAKCSQFC TTGMDGGMSI WDVRSLESAL KDLKIV |
-分子 #4: Actin-related protein 2/3 complex subunit 2, ArpC2
分子 | 名称: Actin-related protein 2/3 complex subunit 2, ArpC2 / タイプ: protein_or_peptide / ID: 4 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 34.402043 KDa |
配列 | 文字列: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV ...文字列: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV FKDDDDVVIG KVFMQEFKEG RRASHTAPQV LFSHREPPLE LKDTDAAVGD NIGYITFVLF PRHTNASARD NT INLIHTF RDYLHYHIKC SKAYIHTRMR AKTSDFLKVL NRARPDAEKK EMKTITGKTF SSR |
-分子 #5: Actin-related protein 2/3 complex subunit 3, ArpC3
分子 | 名称: Actin-related protein 2/3 complex subunit 3, ArpC3 / タイプ: protein_or_peptide / ID: 5 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 20.572666 KDa |
配列 | 文字列: MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF MNKSLSGPGQ |
-分子 #6: Actin-related protein 2/3 complex subunit 4, ArpC4
分子 | 名称: Actin-related protein 2/3 complex subunit 4, ArpC4 / タイプ: protein_or_peptide / ID: 6 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 19.697047 KDa |
配列 | 文字列: MTATLRPYLS AVRATLQAAL CLENFSSQVV ERHNKPEVEV RSSKELLLQP VTISRNEKEK VLIEGSINSV RVSIAVKQAD EIEKILCHK FMRFMMMRAE NFFILRRKPV EGYDISFLIT NFHTEQMYKH KLVDFVIHFM EEIDKEISEM KLSVNARARI V AEEFLKNF |
-分子 #7: Actin-related protein 2/3 complex subunit 5, ArpC5
分子 | 名称: Actin-related protein 2/3 complex subunit 5, ArpC5 / タイプ: protein_or_peptide / ID: 7 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 16.295317 KDa |
配列 | 文字列: MSKNTVSSAR FRKVDVDEYD ENKFVDEDDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAVLLQWH EKALAAGGVG SIVRVLTARK TV |
-分子 #8: Actin, alpha skeletal muscle, ACTA1
分子 | 名称: Actin, alpha skeletal muscle, ACTA1 / タイプ: protein_or_peptide / ID: 8 詳細: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even ...詳細: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. コピー数: 11 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 42.096953 KDa |
配列 | 文字列: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...文字列: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | サブトモグラム平均法 |
試料の集合状態 | cell |
-試料調製
緩衝液 | pH: 6.1 構成要素:
詳細: Adjust to pH 6.1 using NaOH | ||||||||||||
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グリッド | モデル: Quantifoil R2/2 / 材質: GOLD / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 120 sec. / 前処理 - 雰囲気: AIR 詳細: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 80 % / チャンバー内温度: 277 K 詳細: Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均露光時間: 1.21 sec. / 平均電子線量: 2.79 e/Å2 詳細: Images were collected in movie-mode at 7 frames per tilt |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): -0.0055 µm / 最小 デフォーカス(公称値): -0.00175 µm / 倍率(公称値): 42000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||||
得られたモデル | PDB-7aqk: |