- EMDB-9969: Thermococcus kodakarensis RNA polymerase in complex with transcri... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: EMDB / ID: EMD-9969
タイトル
Thermococcus kodakarensis RNA polymerase in complex with transcription factor E, focused refinement on RNAP stalk and clamp domains and TFE
マップデータ
Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko) in complex with transcription factor E (TFE), resulting from focused refinement
試料
複合体: Thermococcus kodakarensis RNA polymerase in complex with transcription factor E
機能・相同性
機能・相同性情報
transcription open complex formation at RNA polymerase II promoter / transcription initiation at RNA polymerase III promoter / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / protein dimerization activity ...transcription open complex formation at RNA polymerase II promoter / transcription initiation at RNA polymerase III promoter / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm 類似検索 - 分子機能
ダウンロード / ファイル: emd_9969.map.gz / 形式: CCP4 / 大きさ: 20.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko) in complex with transcription factor E (TFE), resulting from focused refinement
Movie frame data was subjected to motion correction to generate summed micrographs using MotionCor2.
粒子像選択
選択した数: 1226339 詳細: Approximately 20,000 particles were selected manually. 2D class averages from the manual-picked particles were used as a template for automated particle picking in Relion 2.1.
CTF補正
ソフトウェア - 名称: Gctf (ver. 1.06) 詳細: Defocus parameters were calculated from motion-corrected micrographs, using Gctf 1.06. Using the defocus parameters, Cs (0.003, after Cs image corrector tuning) and amplitude contrast (0.1), ...詳細: Defocus parameters were calculated from motion-corrected micrographs, using Gctf 1.06. Using the defocus parameters, Cs (0.003, after Cs image corrector tuning) and amplitude contrast (0.1), CTF phase flipping and amplitude correction was performed during the reconstruction using Relion 2.1.
詳細: PDB file was converted to EM map using e2pdb2mrc.py routine in EMAN2 software package. The reference map was lowpass filtered to 60 angstroms as a startup model.
最終 再構成
使用したクラス数: 1 / 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: BACK PROJECTION / 解像度のタイプ: BY AUTHOR / 解像度: 4.25 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.1) 詳細: Focused refinement on stalk and clamp domains of RNAP and TFE was performed by continuing the last iteration of the 3D refinement run of the entire structure (EMD-9961), with the applied local mask 使用した粒子像数: 252508
初期 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 2.1)
最終 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 2.1)