登録情報 データベース : PDB / ID : 6kf9 構造の表示 ダウンロードとリンクタイトル Cryo-EM structure of Thermococcus kodakarensis RNA polymerase 要素(DNA-directed RNA polymerase subunit ... ポリメラーゼ ) x 8 (DNA-directed RNA polymerase, subunit ... ポリメラーゼ ) x 2 DNA (27-MER) DNA (5'-D(P*TP*CP*GP*GP*TP*AP*AP*TP*CP*AP*CP*GP*CP*TP*CP*C)-3')DNA-directed RNA polymerase subunit ポリメラーゼ Transcription factor E 残り2件を表示 表示を減らす 詳細キーワード TRANSCRIPTION (転写 (生物学)) / apo-RNA polymerase機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
transcription open complex formation at RNA polymerase II promoter / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription ... transcription open complex formation at RNA polymerase II promoter / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / 細胞質 類似検索 - 分子機能 Alpha-Beta Plaits - #3110 / Helix Hairpins - #10 / Transcription factor TFE, archaea / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / HRDC domain ... Alpha-Beta Plaits - #3110 / Helix Hairpins - #10 / Transcription factor TFE, archaea / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / HRDC domain / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Helix Hairpins / Gyrase A; domain 2 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / Helix non-globular / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain 類似検索 - ドメイン・相同性 デオキシリボ核酸 / DNA (> 10) / Transcription factor E / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo4 ... デオキシリボ核酸 / DNA (> 10) / Transcription factor E / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo3 類似検索 - 構成要素生物種 Thermococcus kodakarensis KOD1 (古細菌)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 : 3.79 Å 詳細データ登録者 Jun, S.-H. / Hyun, J. / Jeong, H. / Cha, J.S. / Kim, H. / Bartlett, M.S. / Cho, H.-S. / Murakami, K.S. 資金援助 韓国, 米国, 4件 詳細 詳細を隠す組織 認可番号 国 Ministry of Education (Korea) 2015R1D1A1A01059097 韓国 Ministry of Science, ICT and Future Planning NRF-2017M3A9F6029755 韓国 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM131860 米国 National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) R15 GM083306 米国
引用ジャーナル : Nat Commun / 年 : 2020タイトル : Direct binding of TFEα opens DNA binding cleft of RNA polymerase.著者 : Sung-Hoon Jun / Jaekyung Hyun / Jeong Seok Cha / Hoyoung Kim / Michael S Bartlett / Hyun-Soo Cho / Katsuhiko S Murakami / 要旨 : Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron ... Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs. 履歴 登録 2019年7月7日 登録サイト : PDBJ / 処理サイト : PDBJ改定 1.0 2020年7月1日 Provider : repository / タイプ : Initial release改定 1.1 2020年12月23日 Group : Database references / カテゴリ : database_2 / pdbx_database_relatedItem : _database_2.database_code / _pdbx_database_related.content_type改定 1.2 2021年1月13日 Group : Database references / カテゴリ : citation / citation_authorItem : _citation.country / _citation.journal_abbrev ... _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year 改定 1.3 2022年3月23日 Group : Author supporting evidence / Database references / カテゴリ : database_2 / pdbx_audit_supportItem : _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization改定 1.4 2024年5月29日 Group : Data collection / カテゴリ : chem_comp_atom / chem_comp_bond
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