- EMDB-40083: E. coli clamp loader with closed clamp on primed template DNA -
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基本情報
登録情報
データベース: EMDB / ID: EMD-40083
タイトル
E. coli clamp loader with closed clamp on primed template DNA
マップデータ
CLC.DNA.Beta2 Closed
試料
複合体: E. coli clamp loader with closed clamp on primed template DNA
タンパク質・ペプチド: x 5種
DNA: x 2種
リガンド: x 4種
キーワード
clamp loader / DNA clamp / AAA+ / ATPase / DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報
DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA clamp loader activity / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity ...DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA clamp loader activity / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / response to radiation / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol 類似検索 - 分子機能
DNA polymerase III, psi subunit / DNA polymerase III, psi subunit, subgroup / DNA polymerase III, psi subunit superfamily / DNA polymerase III psi subunit / DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal ...DNA polymerase III, psi subunit / DNA polymerase III, psi subunit, subgroup / DNA polymerase III, psi subunit superfamily / DNA polymerase III psi subunit / DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / DNA polymerase III, delta subunit / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / ClpA/B family / : / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase 類似検索 - ドメイン・相同性
DNA polymerase III subunit tau / Beta sliding clamp / DNA polymerase III subunit delta / DNA polymerase III subunit delta' / DNA polymerase III subunit psi 類似検索 - 構成要素
全体 : E. coli clamp loader with closed clamp on primed template DNA
全体
名称: E. coli clamp loader with closed clamp on primed template DNA
要素
複合体: E. coli clamp loader with closed clamp on primed template DNA
タンパク質・ペプチド: DNA polymerase III subunit delta
タンパク質・ペプチド: DNA polymerase III subunit tau
タンパク質・ペプチド: DNA polymerase III subunit delta'
タンパク質・ペプチド: DNA polymerase III subunit psi
タンパク質・ペプチド: Beta sliding clamp
DNA: Primer
DNA: Template
リガンド: ADENOSINE-5'-DIPHOSPHATE
リガンド: MAGNESIUM ION
リガンド: TETRAFLUOROALUMINATE ION
リガンド: ZINC ION
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超分子 #1: E. coli clamp loader with closed clamp on primed template DNA
超分子
名称: E. coli clamp loader with closed clamp on primed template DNA タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#7 詳細: Clamp loader complex composed of DNA polymerase III delta tau(3) delta' chi and psi subunits. Clamp composed of DNA polymerase III beta(2) subunits.
由来(天然)
生物種: Escherichia coli (大腸菌) / 株: K-12
分子量
理論値: 419 KDa
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分子 #1: DNA polymerase III subunit delta
分子
名称: DNA polymerase III subunit delta / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: DNA-directed DNA polymerase
詳細: 30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
グリッド
モデル: UltrAuFoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: GOLD / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 時間: 120 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.03 kPa 詳細: Used a Zepto Low-pressure plasma systems (PLASMA CLEANER) (Diener Electronic) at 10% power for 120 seconds.
凍結
凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 279 K / 装置: FEI VITROBOT MARK IV 詳細: 3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane..
詳細
30 microL of 6.0 microM delta/tau3/delta' complex was mixed with chi/psi complex, beta, and p/t DNA (annealed DNA oligonucleotides) at a molar ratio of 1:1.3 and dialysed at 4 degrees C against 250 mL of 30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1)
最終 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1)
最終 3次元分類
クラス数: 4 / 平均メンバー数/クラス: 120000 / ソフトウェア - 名称: RELION (ver. 3.1) 詳細: Most particles were classified to two classes that were used for final 3D reconstruction.