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- PDB-6z9s: Transcription termination intermediate complex 4 -

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基本情報

登録情報
データベース: PDB / ID: 6z9s
タイトルTranscription termination intermediate complex 4
要素
  • (DNA-directed RNA polymerase subunit ...) x 4
  • (Transcription ...) x 2
  • non template strand
  • rut RNA
  • template strand
キーワードTRANSCRIPTION / Termination / Helicase / RNA Polymerase
機能・相同性
機能・相同性情報


ATP-dependent activity, acting on RNA / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / protein complex oligomerization / bacterial-type flagellum-dependent cell motility ...ATP-dependent activity, acting on RNA / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / protein complex oligomerization / bacterial-type flagellum-dependent cell motility / nitrate assimilation / translation elongation factor activity / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / helicase activity / DNA-templated transcription termination / 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 / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity / protein domain specific binding / response to antibiotic / nucleotide binding / DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Transcription termination factor Rho / Rho termination factor, N-terminal ...Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / DNA repair Rad51/transcription factor NusA, alpha-helical / Type-1 KH domain profile. / Helix-hairpin-helix domain / S1 domain profile. / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / 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 / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Transcription termination factor Rho / DNA-directed RNA polymerase subunit beta' / Transcription termination/antitermination protein NusA / DNA-directed RNA polymerase subunit alpha ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Transcription termination factor Rho / DNA-directed RNA polymerase subunit beta' / Transcription termination/antitermination protein NusA / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta / Transcription termination/antitermination protein NusA / Transcription termination factor Rho
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
synthetic construct (人工物)
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: 4.4 Å
データ登録者Said, N. / Hilal, T. / Loll, B. / Wahl, M.C.
資金援助 ドイツ, 3件
組織認可番号国
German Research Foundation (DFG)RTG 2473-1 ドイツ
German Research Foundation (DFG)WA 1126/11-1 ドイツ
German Federal Ministry for Education and Research01DQ20006 ドイツ
引用ジャーナル: Science / 年: 2021
タイトル: Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ.
著者: Nelly Said / Tarek Hilal / Nicholas D Sunday / Ajay Khatri / Jörg Bürger / Thorsten Mielke / Georgiy A Belogurov / Bernhard Loll / Ranjan Sen / Irina Artsimovitch / Markus C Wahl /
要旨: Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ...Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ρ on a pathway to terminating NusA/NusG-modified elongation complexes. An open ρ ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the ρ ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase zinc-binding domain, NusA rotates underneath one capping ρ subunit, which subsequently captures RNA. After detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that ρ, and other termination factors across life, may use analogous strategies to allosterically trap transcription complexes in a moribund state.
履歴
登録2020年6月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年11月4日Provider: repository / タイプ: Initial release
改定 1.12021年2月3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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-11090
  • 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
f: Transcription termination factor Rho
a: Transcription termination factor Rho
b: Transcription termination factor Rho
c: Transcription termination factor Rho
d: Transcription termination factor Rho
e: Transcription termination factor Rho
A: Transcription termination/antitermination protein NusA
U: DNA-directed RNA polymerase subunit alpha
V: DNA-directed RNA polymerase subunit alpha
W: DNA-directed RNA polymerase subunit omega
X: DNA-directed RNA polymerase subunit beta
Y: DNA-directed RNA polymerase subunit beta'
K: non template strand
L: template strand
R: rut RNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)793,39733
ポリマ－790,65415
非ポリマー2,74318
水27015
1


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

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要素

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Transcription ... , 2種, 7分子 fabcdeA

#1: タンパク質
Transcription termination factor Rho / ATP-dependent helicase Rho


分子量: 47070.168 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: rho, AC789_1c41660, ACN002_3874, EL75_4398, EL79_4648, EL80_4555
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: A0A0A0GPI6, UniProt: P0AG30*PLUS, 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
#2: タンパク質 Transcription termination/antitermination protein NusA


分子量: 55060.812 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: nusA, A6581_13525, A8C65_02280, A9819_18195, A9R57_12710, A9X72_02950, AC789_1c35390, ACN002_3262, ACN68_12470, ACN81_18560, ACU57_14555, ACU90_11675, AJ318_05130, AM270_15620, AM464_ ...遺伝子: nusA, A6581_13525, A8C65_02280, A9819_18195, A9R57_12710, A9X72_02950, AC789_1c35390, ACN002_3262, ACN68_12470, ACN81_18560, ACU57_14555, ACU90_11675, AJ318_05130, AM270_15620, AM464_08470, AM465_07745, AMK83_06450, AML35_13995, ARC77_12295, AU473_05845, AUQ13_02965, AW059_15285, AWB10_02965, AWE53_007755, AWF59_011800, AWG78_015835, AZZ83_001443, B6V57_17910, B7C53_06460, B9N33_16970, BANRA_01789, BANRA_03826, BB545_09890, BFD68_02465, BHF03_08610, BHF46_07205, BHS87_17855, BIQ87_17925, BIU72_05295, BIZ41_14490, BJJ90_02880, BK373_10285, BK375_17175, BK383_15855, BMT91_09130, BN17_31141, BOH76_04800, BON63_14350, BON65_19800, BON66_12095, BON69_26670, BON71_25285, BON72_14050, BON75_23260, BON76_05640, BON94_12450, BON95_22130, BON96_06470, BTQ04_16590, BTQ06_11760, BUE81_19575, BvCms12BK_01027, BvCms2454_04844, BvCms28BK_03352, BvCms35BK_01521, BvCmsC61A_01481, BvCmsHHP001_01224, BvCmsHHP019_03131, BvCmsHHP056_02506, BvCmsKKP036_00266, BvCmsKKP061_00866, BvCmsKSNP073_02140, BvCmsKSNP081_00264, BvCmsKSNP120_03552, BvCmsKSP011_02072, BvCmsKSP024_00305, BvCmsKSP026_00480, BvCmsKSP045_01628, BvCmsKSP058_01862, BvCmsKSP067_01442, BvCmsKSP076_01608, BvCmsNSNP036_02129, BvCmsNSP006_04618, BvCmsNSP007_02229, BvCmsNSP047_04140, BvCmsOUP014_03610, BvCmsSINP011_04480, BvCmsSINP022_03541, BvCmsSIP019_00385, BvCmsSIP044_00115, BW690_05715, BWI89_22180, BWP17_10040, BXT93_11865, BZL31_05810, C2U48_17660, C4K41_03670, C5N07_18180, C5P44_00540, C7B06_16690, C7B07_10710, C9098_07900, C9114_15345, C9162_04220, C9E25_11380, C9E67_03485, C9Z23_02315, C9Z28_00495, C9Z29_07080, C9Z37_14770, C9Z39_14385, C9Z69_11065, C9Z70_06875, C9Z78_03425, CCZ14_12145, CCZ17_15255, CF006_16780, CG692_07185, CI693_03560, CI694_20950, CIG45_16160, CMR93_08950, CO706_14520, COD46_10645, CR538_03185, CR539_21135, CRD98_04825, CRM83_23610, CRT43_19205, CT146_02945, CUB99_16245, CVH05_10890, D2184_10395, D2185_00555, D3821_08435, D3C88_08620, D3O91_07735, D3Y67_18400, D4M06_11115, D6X76_04225, D7K63_12110, D7Y10_03480, D9D20_06165, D9D31_09845, D9D33_00520, D9E34_10725, D9E35_01735, D9E49_09485, D9F17_07090, D9G42_16790, D9H53_01085, D9H68_07450, D9H70_01530, D9I18_07065, D9I87_04950, D9I88_16540, D9I97_11390, D9J11_01020, D9J44_07740, D9J46_20540, D9J78_05020, D9K54_17930, D9L99_02550, DAH26_17205, DAH30_12985, DAH34_01870, DAH37_04365, DAH43_16670, DD762_19130, DEN89_09295, DEN97_16025, DEO04_19495, DEO19_06320, DJ487_12875, DJ503_10865, DL455_12590, DL545_03770, DMI04_04160, DMZ50_12310, DN627_01240, DN700_04485, DNB37_13595, DNR41_11075, DOY56_12135, DP258_01950, DQF57_03505, DQO13_01185, DS732_23585, DS966_19180, DTL43_04185, DTL90_07460, DTM10_07095, DU333_16810, DW236_11975, DXT69_05630, DXT71_00550, DXT73_13270, DXX80_009480, E0I42_14230, E0L04_19775, E2119_05760, E2127_02465, E2128_02605, E2129_05650, E2134_15705, E2135_07970, E5P22_12885, E5P28_13020, E5P37_13245, E5S42_11905, E5S47_02870, E5S61_05815, EA223_04935, EA250_06525, EA834_14925, EAI42_15045, EAI52_10000, EAX79_13120, EB509_07090, EB510_12295, EC1094V2_475, EC3234A_53c00480, EC382_14545, ECs4050, ECTO124_00620, ECTO6_00587, ED225_04160, ED607_10315, ED611_04170, ED648_02805, EF173_16895, EGT48_12340, EI021_03955, EI028_15160, EI032_08695, EIA21_02770, EIZ93_15765, EL75_0516, EL79_0538, EL80_0529, ELT20_05155, ELT23_06875, ELT33_08795, ELT34_10430, ELT48_07010, ELU82_09405, ELU96_15075, ELV05_02165, ELV13_06455, ELV24_06465, ELX79_02850, ELX83_01985, ELY05_03160, ELY23_12925, ELY24_06185, ELY50_10980, EO241_09470, EPS76_01475, EPS94_08345, EPT01_00525, EQ825_16425, ERS085365_00562, ERS085374_01906, ERS085379_00395, ERS085383_00719, ERS085386_00510, ERS085404_02209, ERS085406_02909, ERS085416_00332, ERS139211_00573, ERS150873_04324, EWK56_02885, EXM29_19885, ExPECSC065_00153, EXX06_09580, EXX13_07225, EXX55_08945, EXX71_13290, EXX78_16840, EXX87_04480, EYD11_02755, EYX82_02345, EYX99_26665, EYY34_08675, F1E19_22155, F7F18_01095, F7G01_14090, F7G03_16260, FKO60_06130, FNJ67_03685, FORC82_0590, FQ915_16570, FQR64_03145, FQU83_04620, FRV13_20655, FV293_08485, FV438_11000, FY127_14855, FZ043_21925, HmCms184_00231, HmCmsJML079_04422, HmCmsJML146_01153, HmCmsJML204_02228, HW43_20805, MJ49_14455, MS8345_03518, NCTC10089_00629, NCTC10090_03662, NCTC10767_01660, NCTC10865_00813, NCTC10974_00712, NCTC11022_03334, NCTC11126_02933, NCTC11341_01740, NCTC13127_00931, NCTC8179_06097, NCTC8621_00649, NCTC8959_03134, NCTC9045_00717, NCTC9055_02514, NCTC9058_01244, NCTC9062_02552, NCTC9075_00900, NCTC9081_01077, NCTC9111_00998, NCTC9119_00655, NCTC9434_00566, NCTC9701_00709, NCTC9703_05100, NCTC9706_02868, NCTC9969_00791, PGD_03947, PU06_19960, RG28_20965, RK56_014720, RX35_04256, SAMEA3472044_03332, SAMEA3472047_01872, SAMEA3472055_00400, SAMEA3472056_03072, SAMEA3472080_00945, SAMEA3472090_00548, SAMEA3472108_00102, SAMEA3472114_00483, SAMEA3472147_01878, SAMEA3485101_01710, SAMEA3752553_01187, SAMEA3752557_01875, SAMEA3752559_03273, SAMEA3752620_02341, SAMEA3753064_02936, SAMEA3753097_03302, SAMEA3753164_02300, SAMEA3753290_00148, SAMEA3753300_02131, SK85_03482, SY51_18275, U12A_03405, U14A_03402, UC41_24435, UN86_15490, UN91_15505, WQ89_06750, WR15_24550
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: C3SSN7, UniProt: P0AFF6*PLUS

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DNA-directed RNA polymerase subunit ... , 4種, 5分子 UVWXY

#3: タンパク質 DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


分子量: 36558.680 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: rpoA, pez, phs, sez, b3295, JW3257
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: P0A7Z4, DNA-directed RNA polymerase
#4: タンパク質 DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


分子量: 10249.547 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: rpoZ, b3649, JW3624
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: P0A800, DNA-directed RNA polymerase
#5: タンパク質 DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


分子量: 150820.875 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: rpoB, Z5560, ECs4910
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: P0A8V4, UniProt: P0A8V2*PLUS, DNA-directed RNA polymerase
#6: タンパク質 DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


分子量: 156537.031 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: rpoC, A6581_23995, A6592_25550, A6V01_22675, A8C65_22170, A9P13_25145, A9R57_05210, A9X72_23915, AC789_1c43830, ACN002_4075, ACN68_05320, ACN81_23175, ACU57_23185, ACU90_26200, AM270_ ...遺伝子: rpoC, A6581_23995, A6592_25550, A6V01_22675, A8C65_22170, A9P13_25145, A9R57_05210, A9X72_23915, AC789_1c43830, ACN002_4075, ACN68_05320, ACN81_23175, ACU57_23185, ACU90_26200, AM270_23445, AM446_26250, AM464_13270, AMK83_15405, AML07_02735, AML35_27125, APT94_08715, APZ14_17345, ARC77_17020, AU473_00845, AUQ13_12340, AUS26_26460, AW059_24210, AWB10_24945, AWE53_003330, AWG90_024870, AZZ83_004736, B7C53_21460, B9M99_23215, BANRA_02658, BANRA_02959, BANRA_04874, BANRA_05060, BB545_03160, BE963_11280, BHF03_13085, BHF46_21990, BHS81_23830, BHS87_22295, BIQ87_22860, BIU72_18810, BIZ41_20460, BJJ90_25120, BK292_28025, BK296_22655, BK373_27210, BK375_25315, BK383_27720, BMT49_21005, BMT91_03285, BN17_39521, BOH76_00535, BON63_20110, BON65_15085, BON66_14380, BON69_07675, BON71_08940, BON72_17275, BON75_02240, BON76_16220, BON83_01620, BON87_25670, BON91_27070, BON92_00590, BON94_22185, BON95_12860, BON96_11000, BTQ04_24495, BTQ06_27265, BUE81_05360, BvCms12BK_01429, BvCms2454_04769, BvCms28BK_04518, BvCms35BK_02095, BvCmsC61A_02150, BvCmsHHP001_05236, BvCmsHHP019_04451, BvCmsHHP056_02607, BvCmsKKP061_02982, BvCmsKSNP073_02854, BvCmsKSNP081_04479, BvCmsKSNP120_03436, BvCmsKSP011_02756, BvCmsKSP024_02908, BvCmsKSP026_03362, BvCmsKSP045_04187, BvCmsKSP058_05144, BvCmsKSP067_02566, BvCmsNSNP036_01157, BvCmsNSP006_02615, BvCmsNSP007_05019, BvCmsNSP047_00271, BvCmsNSP072_02893, BvCmsOUP014_03200, BvCmsSINP011_03932, BvCmsSINP022_04155, BvCmsSIP019_00812, BvCmsSIP044_03274, BVL39_05360, BW690_26755, BWI89_17380, BWP17_22705, BXT93_12730, BZL31_04385, BZL69_05725, C2U48_12715, C5715_03850, C5N07_24540, C5P01_26050, C5P44_24170, C7235_23705, C7B02_25785, C7B06_24625, C7B07_24550, C7B08_25760, C9098_22155, C9114_22905, C9141_23610, C9160_23380, C9162_26345, C9201_22200, C9306_18300, C9E25_22085, C9E67_28655, C9Z03_20320, C9Z23_22490, C9Z28_21990, C9Z29_22175, C9Z37_20920, C9Z39_11515, C9Z43_22460, C9Z69_21605, C9Z70_22865, CA593_06020, CDC27_21560, CF006_23865, CI641_013325, CI693_09915, CI694_22465, CIG45_23820, CJU63_23545, CMR93_21720, CO706_19510, COD30_25650, COD46_23645, CR538_24210, CR539_01675, CRD98_23235, CRE06_23980, CRM83_18625, CRX46_23050, CV83915_02065, CVH05_03875, CWS33_24550, D0X26_26125, D2184_25090, D2185_24280, D2188_26590, D3821_09095, D3822_07080, D3O91_23490, D3P01_24335, D3Y67_18045, D4M06_24790, D6T60_24455, D6X76_25460, D7K63_24300, D7K66_23610, D9D20_23630, D9D31_17430, D9D43_22315, D9E34_21770, D9E35_23870, D9F17_24240, D9G48_16815, D9H53_22620, D9H68_20330, D9H70_22065, D9H94_18950, D9I18_21370, D9I87_21145, D9I88_19005, D9I97_19385, D9J03_21580, D9J11_22220, D9J44_24520, D9J60_24650, D9J78_24495, D9K48_24885, D9L89_22865, D9X97_23575, DAH18_24925, DAH26_25940, DAH30_23845, DAH34_21555, DAH37_22570, DAH43_24880, DBQ99_24540, DD762_22280, DEN89_26510, DEN97_23710, DEO04_24305, DEO19_24555, DIV22_03745, DJ487_24740, DJ503_21515, DL455_22980, DL545_23680, DLW88_24480, DM102_24810, DMI04_23195, DN627_23155, DN700_22970, DNB37_22370, DND16_22020, DOY56_23525, DP258_23435, DP277_21385, DQE83_24465, DQF57_23790, DQO13_23780, DTL43_13700, DTL90_24530, DTM10_25855, DU309_24205, DU321_23425, DW236_24545, DXT69_22805, DXT71_22310, DXT73_22940, DXX80_014100, E0I42_21900, E0K84_22885, E0L12_22045, E2112_20360, E2119_22340, E2127_20900, E2128_03185, E2129_21295, E2134_22790, E2135_19330, E4K55_23345, E5P22_12650, E5P28_08825, E5P37_21450, E5S42_21540, E5S47_23025, E5S58_21685, E5S61_22375, EA223_18745, EA410_23470, EAI42_07590, EAI46_11695, EAI52_22800, EAX79_24760, EB509_19940, EB510_23045, EB515_23245, EC1094V2_4282, EC3234A_76c00080, EC3426_00300, EC382_20005, ECs4911, ECTO6_04517, ED225_22845, ED607_18495, ED611_23935, ED648_18905, ED903_15585, ED944_23315, EEA45_21100, EEP23_09490, EF173_24455, EHH55_00715, EHJ36_22705, EI021_22070, EI028_22520, EI032_21250, EIA21_22525, EIZ93_16335, EJC75_19635, EL75_4201, EL79_4407, EL80_4314, ELT20_20720, ELT23_22660, ELU85_23590, ELV08_18690, ELV28_22250, ELY05_18165, EO241_25775, EPT01_21680, EQ820_22870, EQ823_21565, ERS085365_04275, ERS085366_03840, ERS085374_04587, ERS085379_04695, ERS085383_04736, ERS085386_04630, ERS085404_04514, ERS085416_04248, ERS139211_00022, ERS150873_04406, ERS150876_04849, EST51_23860, EVY14_16840, EXM29_02400, EXX06_24525, EXX23_22305, EXX24_23170, EXX53_21005, EXX55_24440, EXX71_22255, EXX78_24010, EXX87_24980, EYD11_21590, EYX82_16690, EYY34_19805, EYY78_22660, F1E13_23750, F1E19_21825, F7F11_23815, F7F18_24055, F7F29_25930, F7G01_23350, F7G03_24075, FAF34_028960, FNJ69_19110, FNJ83_24800, FORC82_4521, FQ915_26150, FQR64_21800, FRV13_16215, FV293_23430, FV438_22435, FWK02_01680, FY127_17750, FZ043_01140, GJ11_25200, HmCms184_03861, HmCmsJML074_03182, HmCmsJML079_04902, HmCmsJML204_03257, HMPREF3040_01778, HW43_01585, MJ49_09425, NCTC10082_02080, NCTC10090_02779, NCTC10429_00081, NCTC10865_05894, NCTC10974_05350, NCTC11181_01964, NCTC12950_05213, NCTC13127_06163, NCTC13148_04414, NCTC7927_05248, NCTC8500_05324, NCTC8960_02339, NCTC9036_04648, NCTC9044_02305, NCTC9045_05541, NCTC9050_02817, NCTC9055_01666, NCTC9058_02148, NCTC9062_03445, NCTC9077_05932, NCTC9111_04954, NCTC9119_05054, NCTC9701_04995, NCTC9706_02002, NCTC9777_01117, NCTC9969_04931, PGD_00622, PU06_15490, RG28_25345, RK56_017400, RX35_03755, SAMEA3472043_04866, SAMEA3472044_04873, SAMEA3472047_03500, SAMEA3472055_04947, SAMEA3472056_05309, SAMEA3472070_05093, SAMEA3472080_04815, SAMEA3472090_05006, SAMEA3472108_04971, SAMEA3472110_05082, SAMEA3472112_05167, SAMEA3472114_04967, SAMEA3472147_04120, SAMEA3484427_04984, SAMEA3484429_04987, SAMEA3484434_04725, SAMEA3485101_05497, SAMEA3485113_04495, SAMEA3752372_05079, SAMEA3752553_04905, SAMEA3752557_04844, SAMEA3752559_04855, SAMEA3752620_04699, SAMEA3753064_05329, SAMEA3753097_04845, SAMEA3753164_04786, SAMEA3753290_00018, SAMEA3753300_04884, SK85_04319, UC41_25650, UN86_14180, UN91_25445, WQ89_24675, WR15_01490, YDC107_2702
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: C3SIA2, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase

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DNA鎖 , 2種, 2分子 KL

#7: DNA鎖 non template strand


分子量: 15541.960 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#8: DNA鎖 template strand


分子量: 15211.717 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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RNA鎖 , 1種, 1分子 R

#9: RNA鎖 rut RNA


分子量: 31693.904 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: Sequences missing due to wrong alignment / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 5種, 33分子

#10: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#11: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mg
#12: 化合物
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


分子量: 66.007 Da / 分子数: 5 / 由来タイプ: 合成 / 式: BeF3
#13: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#14: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 15 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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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: multi subunit DNA/RNA complex / タイプ: COMPLEX / Entity ID: #1-#9 / 由来: RECOMBINANT
分子量値: 0.67 MDa / 実験値: NO
由来(天然)生物種: Escherichia coli (大腸菌)
由来(組換発現)生物種: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
緩衝液pH: 7.5
試料濃度: 5 mg/ml / 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: Tecnai Polara / 画像提供: FEI Company
顕微鏡モデル: FEI POLARA 300
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
撮影電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)

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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
2Leginon3.3画像取得
4CTFFIND4CTF補正
10cryoSPARC2.12初期オイラー角割当
11cryoSPARC2.14最終オイラー角割当
12cisTEM分類
13cryoSPARC2.14３次元再構成
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: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 24950 / 対称性のタイプ: POINT

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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

他の情報も見る