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- PDB-9ei3: Cryo-EM structure of Human RNA polymerase II Elongation Complex b... -

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基本情報

登録情報
データベース: PDB / ID: 9ei3
タイトルCryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP
要素
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • ATP-dependent DNA helicase Q5
  • Non-template DNA, nucleic acid scaffold
  • RNA, nucleic acid scaffold
  • Template DNA, nucleic acid scaffold
キーワードTRANSCRIPTION / TRANSFERASE/DNA/RNA / translocation / Human RNA polymerase II / RECQL5 helicase / TRANSFERASE-DNA-RNA complex
機能・相同性
機能・相同性情報


mitotic DNA-templated DNA replication / microfibril binding / chromosome separation / cellular response to camptothecin / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / four-way junction helicase activity / regulation of transcription by RNA polymerase I / replication-born double-strand break repair via sister chromatid exchange / RPAP3/R2TP/prefoldin-like complex ...mitotic DNA-templated DNA replication / microfibril binding / chromosome separation / cellular response to camptothecin / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / four-way junction helicase activity / regulation of transcription by RNA polymerase I / replication-born double-strand break repair via sister chromatid exchange / RPAP3/R2TP/prefoldin-like complex / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / Cytosolic sensors of pathogen-associated DNA / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / DNA 3'-5' helicase / LRR domain binding / DNA metabolic process / 3'-5' DNA helicase activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase II complex binding / Processing of Capped Intron-Containing Pre-mRNA / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / transcription by RNA polymerase III / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of double-strand break repair via homologous recombination / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / transcription-coupled nucleotide-excision repair / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / DNA helicase activity / Inhibition of DNA recombination at telomere / positive regulation of RNA splicing / replication fork / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / P-body / Transcriptional regulation by small RNAs / DNA-templated transcription termination / helicase activity / protein-DNA complex / double-strand break repair via homologous recombination / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / ribonucleoside binding / cellular response to xenobiotic stimulus / Activation of anterior HOX genes in hindbrain development during early embryogenesis / fibrillar center / Dual incision in TC-NER / DNA-directed RNA polymerase / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / mitotic cell cycle / single-stranded DNA binding / chromosome
類似検索 - 分子機能
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / 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 / 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, 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / Helicase conserved C-terminal domain / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / ATP-dependent DNA helicase Q5 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB1 ...PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / ATP-dependent DNA helicase Q5 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC5
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 3.2 Å
データ登録者Florez Ariza, A. / Lue, N. / Nogales, E.
資金援助 米国, 2件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R35 GM127018 米国
引用
ジャーナル: Nat Struct Mol Biol / 年: 2025
タイトル: Structural insights into transcriptional regulation by the helicase RECQL5.
著者: Alfredo Jose Florez Ariza / Nicholas Z Lue / Patricia Grob / Benjamin Kaeser / Jie Fang / Susanne A Kassube / Eva Nogales /
要旨: Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA ...Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.
#1: ジャーナル: bioRxiv / 年: 2025
タイトル: Structural insights into transcriptional regulation by the helicase RECQL5.
著者: Alfredo Jose Florez Ariza / Nicholas Z Lue / Patricia Grob / Benjamin Kaeser / Jie Fang / Susanne A Kassube / Eva Nogales /
要旨: Transcription and its regulation pose a major challenge for genome stability. The helicase RECQL5 has been proposed as an important factor to help safeguard the genome, and is the only member of the ...Transcription and its regulation pose a major challenge for genome stability. The helicase RECQL5 has been proposed as an important factor to help safeguard the genome, and is the only member of the human RecQ helicase family that directly binds to RNA Polymerase II (Pol II) and affects its progression. RECQL5 mitigates transcription stress and genome instability in cells, yet the molecular mechanism underlying this phenomenon is unclear. Here, we employ cryo-electron microscopy (cryo-EM) to determine the structures of stalled Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that RECQL5 can modulate the Pol II translocation state. In its nucleotide-free state, RECQL5 mechanically twists the downstream DNA in the EC, and upon nucleotide binding, it undergoes a conformational change that allosterically induces Pol II towards a post-translocation state. We propose this mechanism may help restart Pol II elongation and therefore contribute to reduction of transcription stress.
履歴
登録2024年11月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年3月5日Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: EM metadata / Data content type: EM metadata / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: FSC / Data content type: FSC / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / タイプ: Initial release
改定 1.02025年3月5日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release
改定 1.12025年7月16日Group: Data collection / Database references / カテゴリ: citation / citation_author / em_admin / Item: _em_admin.last_update
改定 1.22025年9月24日Group: Data collection / Database references / カテゴリ: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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構造の表示

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
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11-a
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
N: Non-template DNA, nucleic acid scaffold
P: RNA, nucleic acid scaffold
T: Template DNA, nucleic acid scaffold
U: ATP-dependent DNA helicase Q5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)655,75226
ポリマ－654,69916
非ポリマー1,05410
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_5551

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要素

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DNA-directed RNA polymerase II subunit ... , 7種, 7分子 ABCDGIK

#1: タンパク質 DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


分子量: 217420.047 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P24928, DNA-directed RNA polymerase
#2: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA ...DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA polymerase II subunit 2 / RNA polymerase II subunit B2


分子量: 134071.453 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P30876, DNA-directed RNA polymerase
#3: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA- ...RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA-directed RNA polymerase II subunit C / RPB31


分子量: 31478.148 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P19387
#4: タンパク質 DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa ...RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa subunit / RPB16


分子量: 16331.255 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O15514
#7: タンパク質 DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa ...RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa subunit / RPB19


分子量: 19314.283 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62487
#9: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


分子量: 14541.221 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P36954
#11: タンパク質 DNA-directed RNA polymerase II subunit RPB11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA polymerase II 13.3 kDa subunit


分子量: 13310.284 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P52435

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DNA-directed RNA polymerases I, II, and III subunit ... , 5種, 5分子 EFHJL

#5: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / RPB5 homolog / XAP4


分子量: 24644.318 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P19388
#6: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


分子量: 14491.026 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P61218
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA- ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


分子量: 17162.273 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P52434
#10: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6 / RPB10 homolog


分子量: 7655.123 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62875
#12: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II ...RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


分子量: 7018.244 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P53803

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DNA鎖 , 2種, 2分子 NT

#13: DNA鎖 Non-template DNA, nucleic acid scaffold


分子量: 13305.593 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#15: DNA鎖 Template DNA, nucleic acid scaffold


分子量: 8515.503 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)

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RNA鎖 / タンパク質 , 2種, 2分子 PU

#14: RNA鎖 RNA, nucleic acid scaffold


分子量: 6414.902 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#16: タンパク質 ATP-dependent DNA helicase Q5 / DNA 3'-5' helicase RecQ5 / DNA helicase / RecQ-like type 5 / RecQ5 / RecQ protein-like 5


分子量: 109024.859 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: ATP-dependent DNA helicase Q5 bound to the nucleotide analog AMPPNP (ANP)
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RECQL5, RECQ5 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: O94762, DNA 3'-5' helicase

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非ポリマー , 3種, 10分子

#17: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#18: 化合物 ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#19: 化合物 ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


分子量: 506.196 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H17N6O12P3 / タイプ: SUBJECT OF INVESTIGATION
コメント: AMP-PNP, エネルギー貯蔵分子類似体*YM

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Stalled Human RNA polymerase II Elongation Complex bound to an AMPPNP-bound RECQL5 helicase
タイプ: COMPLEX / Entity ID: #1-#16 / 由来: MULTIPLE SOURCES
分子量値: 0.49 MDa / 実験値: NO
由来(天然)生物種: Homo sapiens (ヒト)
緩衝液pH: 8
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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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: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: OTHER
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 1800 nm / 最小 デフォーカス（公称値）: 800 nm
撮影電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

EMソフトウェア名称: PHENIX / バージョン: 1.20.1_4487 / カテゴリ: モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 80622 / 対称性のタイプ: POINT
精密化交差検証法: NONE

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万見について

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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。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

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

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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