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- PDB-7aqk: Model of the actin filament Arp2/3 complex branch junction in cells -

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基本情報

登録情報
データベース: PDB / ID: 7aqk
タイトルModel of the actin filament Arp2/3 complex branch junction in cells
要素
  • (Actin-related protein ...) x 7
  • Actin, alpha skeletal muscle, ACTA1
キーワードSTRUCTURAL PROTEIN / Actin / Arp2-3 complex / Cytoskeleton
機能・相同性
機能・相同性情報


podosome core / apical ectoplasmic specialization / basal ectoplasmic specialization / actin filament branch point / ventral surface of cell / microtubule organizing center localization / peripheral region of growth cone / negative regulation of bleb assembly / apical tubulobulbar complex / tubulobulbar complex ...podosome core / apical ectoplasmic specialization / basal ectoplasmic specialization / actin filament branch point / ventral surface of cell / microtubule organizing center localization / peripheral region of growth cone / negative regulation of bleb assembly / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / concave side of sperm head / lamellipodium organization / positive regulation of barbed-end actin filament capping / meiotic cytokinesis / protein kinase C signaling / spindle localization / postsynaptic actin cytoskeleton organization / leading edge of lamellipodium / EPHB-mediated forward signaling / muscle cell projection membrane / RHO GTPases Activate WASPs and WAVEs / hemidesmosome / actin filament network formation / Arp2/3 protein complex / asymmetric cell division / postsynapse organization / Arp2/3 complex-mediated actin nucleation / cellular response to rapamycin / podosome ring / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / actin cap / negative regulation of axon extension / Regulation of actin dynamics for phagocytic cup formation / maintenance of cell polarity / Clathrin-mediated endocytosis / positive regulation of dendritic spine morphogenesis / regulation of actin filament polymerization / positive regulation of astrocyte differentiation / positive regulation of dendrite morphogenesis / apical dendrite / astrocyte differentiation / positive regulation of fibroblast migration / positive regulation of podosome assembly / positive regulation of synapse assembly / podosome / positive regulation of filopodium assembly / smooth muscle cell migration / positive regulation of smooth muscle cell migration / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cell leading edge / filamentous actin / mesenchyme migration / brush border / striated muscle thin filament / skeletal muscle thin filament assembly / cilium assembly / positive regulation of protein targeting to membrane / excitatory synapse / regulation of synaptic vesicle endocytosis / glutamate receptor binding / positive regulation of double-strand break repair via homologous recombination / cellular response to transforming growth factor beta stimulus / positive regulation of lamellipodium assembly / skeletal muscle fiber development / stress fiber / cytoskeletal protein binding / cellular response to platelet-derived growth factor stimulus / axon terminus / ruffle / actin filament polymerization / Neutrophil degranulation / positive regulation of neuron differentiation / positive regulation of substrate adhesion-dependent cell spreading / secretory granule / cellular response to epidermal growth factor stimulus / dendritic shaft / meiotic cell cycle / cell projection / filopodium / positive regulation of protein localization to plasma membrane / actin filament / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / 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 / cellular response to type II interferon / ruffle membrane / synaptic vesicle membrane / actin filament binding / cell migration / cellular response to tumor necrosis factor / cell-cell junction / lamellipodium / presynapse
類似検索 - 分子機能
Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc ...Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2 / Actin, alpha skeletal muscle / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 9 Å
データ登録者Faessler, F. / Dimchev, G. / Hodirnau, V.V. / Wan, W. / Schur, F.K.M.
資金援助 オーストリア, 1件
組織認可番号国
Austrian Science FundP33367 オーストリア
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
登録2020年10月22日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年12月2日Provider: repository / タイプ: Initial release
改定 1.12020年12月30日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22021年1月6日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.32024年5月1日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • マップデータ: EMDB-11869
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-11869
  • UCSF Chimeraによる作画
  • ダウンロード
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

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集合体

登録構造単位
b: Actin-related protein 2, Arp2
a: Actin-related protein 3, Arp3
c: Actin-related protein 2/3 complex subunit 1b, ArpC1b
d: Actin-related protein 2/3 complex subunit 2, ArpC2
e: Actin-related protein 2/3 complex subunit 3, ArpC3
f: Actin-related protein 2/3 complex subunit 4, ArpC4
g: Actin-related protein 2/3 complex subunit 5, ArpC5
h: Actin, alpha skeletal muscle, ACTA1
i: Actin, alpha skeletal muscle, ACTA1
j: Actin, alpha skeletal muscle, ACTA1
k: Actin, alpha skeletal muscle, ACTA1
l: Actin, alpha skeletal muscle, ACTA1
m: Actin, alpha skeletal muscle, ACTA1
n: Actin, alpha skeletal muscle, ACTA1
o: Actin, alpha skeletal muscle, ACTA1
p: Actin, alpha skeletal muscle, ACTA1
q: Actin, alpha skeletal muscle, ACTA1
r: Actin, alpha skeletal muscle, ACTA1


分子量 (理論値)分子数
合計 (水以外)687,29718
ポリマ－687,29718
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_5551

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要素

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Actin-related protein ... , 7種, 7分子 bacdefg

#1: タンパク質 Actin-related protein 2, Arp2


分子量: 44818.711 Da / 分子数: 1 / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: P61161*PLUS
#2: タンパク質 Actin-related protein 3, Arp3


分子量: 47428.031 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus I259V / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: Q99JY9*PLUS
#3: タンパク質 Actin-related protein 2/3 complex subunit 1b, ArpC1b


分子量: 41016.738 Da / 分子数: 1
Mutation: From Bos taurus to Mus Musculus V43N, Q44K, V58I, D63E, K109N, S154N, N213S, A229V, S256N, S274N, G277V, K278T, L296M, S313G, A216T, R360K
由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: Q9WV32*PLUS
#4: タンパク質 Actin-related protein 2/3 complex subunit 2, ArpC2


分子量: 34402.043 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus Y84F, S90P / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: Q9CVB6*PLUS
#5: タンパク質 Actin-related protein 2/3 complex subunit 3, ArpC3


分子量: 20572.666 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus I24L / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: Q9JM76*PLUS
#6: タンパク質 Actin-related protein 2/3 complex subunit 4, ArpC4


分子量: 19697.047 Da / 分子数: 1 / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: P59999*PLUS
#7: タンパク質 Actin-related protein 2/3 complex subunit 5, ArpC5


分子量: 16295.317 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus D28E / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: Q9CPW4*PLUS

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タンパク質 , 1種, 11分子 hijklmnopqr

#8: タンパク質
Actin, alpha skeletal muscle, ACTA1


分子量: 42096.953 Da / 分子数: 11 / 由来タイプ: 天然
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.
由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: NIH-3T3 / 参照: UniProt: P68134*PLUS

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: CELL / ３次元再構成法: サブトモグラム平均法

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試料調製

構成要素名称: Actin Filament Arp2/3 Complex Branch Junction / タイプ: CELL
詳細: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia
Entity ID: all / 由来: NATURAL
由来(天然)生物種: Mus musculus (ハツカネズミ) / 細胞内の位置: Lamellipodium
緩衝液pH: 6.1 / 詳細: Adjust to pH 6.1 using NaOH
緩衝液成分
ID濃度名称Buffer-ID
110 mMMES1
2150 mMsodium chloride1
35 mMEGTA1
45 mMGlucose1
55 mMMagnesium chloride1
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持詳細: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin
グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/2
急速凍結凍結剤: ETHANE / 湿度: 80 % / 凍結前の試料温度: 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

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
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 FIELD / 倍率（公称値）: 42000 X / 最大 デフォーカス（公称値）: -5.5 nm / 最小 デフォーカス（公称値）: -1.75 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: ZEMLIN TABLEAU
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: 1.21 sec. / 電子線照射量: 2.79 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)
詳細: Images were collected in movie-mode at 7 frames per tilt
電子光学装置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

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解析

EMソフトウェア
ID名称バージョンカテゴリ
1Dynamo1.133volume selection
2Warp1.07volume selection
3SerialEM画像取得
5Warp1.07CTF補正
8UCSF Chimera1.13.1モデルフィッティング
11RELION3.0.9最終オイラー角割当
12RELION3.0.9分類
13RELION3.0.9３次元再構成
14ISOLDE1.0b5モデル精密化
15Coot0.8.9.3モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C1 (非対称)
3次元再構成解像度: 9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 14296
詳細: Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9.
クラス平均像の数: 1 / 対称性のタイプ: POINT
EM volume selection手法: Template Matching
詳細: After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained.
Num. of tomograms: 131 / Num. of volumes extracted: 39300
Reference model: Reference generated from manually selected particles
原子モデル構築プロトコル: FLEXIBLE FIT / 空間: REAL
原子モデル構築

3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model

IDPDB-IDPDB chain-IDAccession codeInitial refinement model-IDPdb chain residue range
11TYQ

1tyq

A1TYQ12-39
21TYQ

1tyq

A1TYQ152-353
31TYQ

1tyq

A1TYQ1360-418
41TYQ

1tyq

B1TYQ1151-345
51TYQ

1tyq

C1TYQ11-288
61TYQ

1tyq

C1TYQ1319-372
71TYQ

1tyq

D1TYQ11-208
81TYQ

1tyq

D1TYQ1217-281
91TYQ

1tyq

E1TYQ12-150
101TYQ

1tyq

E1TYQ1155-174
111TYQ

1tyq

F1TYQ13-168
121TYQ

1tyq

G1TYQ136-151
134JD2

4jd2

B4JD224-150
144JD2

4jd2

B4JD22346-387
151K8K

1k8k

C1K8K3297-309
166T20

6t20

A6T2045-375
176T20

6t20

B6T2045-375
186T20

6t20

C6T2045-375
196T20

6t20

D6T2045-375
206T20

6t20

E6T2045-375

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
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関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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