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- PDB-7uio: Mediator-PIC Early (Composite Model) -

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基本情報

登録情報
データベース: PDB / ID: 7uio
タイトルMediator-PIC Early (Composite Model)
要素
  • (DNA-directed RNA polymerase II subunit ...) x 8
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Mediator of RNA polymerase II transcription subunit ...) x 21
  • (Transcription ...) x 4
  • DNA (37-MER)
  • DNA (38-MER)
  • Regulatory protein GAL4
キーワードTRANSCRIPTION / Divergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16
機能・相同性
機能・相同性情報


TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / regulation of transcription from RNA polymerase II promoter by galactose / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / : / transcription open complex formation at RNA polymerase II promoter / TFIIH-class transcription factor complex binding / regulation of mRNA 3'-end processing / galactose metabolic process ...TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / regulation of transcription from RNA polymerase II promoter by galactose / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / : / transcription open complex formation at RNA polymerase II promoter / TFIIH-class transcription factor complex binding / regulation of mRNA 3'-end processing / galactose metabolic process / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RPB4-RPB7 complex / mediator complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / RNA-templated transcription / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / TFIIB-class transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II complex binding / TFIID-class transcription factor complex binding / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / protein phosphatase activator activity / positive regulation of translational initiation / nuclear-transcribed mRNA catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II preinitiation complex assembly / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / transcription repressor complex / transcription-coupled nucleotide-excision repair / translation initiation factor binding / cellular response to nutrient levels / response to endoplasmic reticulum stress / TBP-class protein binding / transcription antitermination / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / P-body / mRNA transcription by RNA polymerase II / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / transcription corepressor activity / peroxisome / single-stranded DNA binding / cellular response to heat / ribosome biogenesis / DNA recombination / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor binding / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein-macromolecule adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity
類似検索 - 分子機能
Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Gal4 dimerisation domain / Gal4-like dimerisation domain / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain ...Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Gal4 dimerisation domain / Gal4-like dimerisation domain / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain / Mediator complex subunit 15, KIX domain / Mediator complex subunit 15 / KIX domain / Gal11 activator-binding domain (ABD1) / : / Mediator complex, subunit Med19, fungi / Fungal specific transcription factor domain / Rox3 mediator complex subunit / Transcription factor domain, fungi / Fungal specific transcription factor domain / Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med7 superfmaily / : / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Zn(2)-C6 fungal-type DNA-binding domain signature. / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Fungal Zn(2)-Cys(6) binuclear cluster domain / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain superfamily / Transcription elongation factor S-II, central domain / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / TFIIS N-terminal domain profile. / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / Coactivator CBP, KIX domain superfamily / TFIIS/LEDGF domain superfamily / Basic-leucine zipper domain superfamily
類似検索 - ドメイン・相同性
ALANINE / ASPARTIC ACID / THREONINE / DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / Regulatory protein GAL4 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 ...ALANINE / ASPARTIC ACID / THREONINE / DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / Regulatory protein GAL4 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 15 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 9 / DNA-directed RNA polymerase II subunit RPB7 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 6 / DNA-directed RNA polymerase II subunit RPB11 / Mediator of RNA polymerase II transcription subunit 3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 5 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 2 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 11
類似検索 - 構成要素
生物種Saccharomyces cerevisiae S288C (パン酵母)
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: 3.3 Å
データ登録者Gorbea Colon, J.J. / Chen, S.-F. / Tsai, K.L. / Murakami, K.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233-01 米国
引用ジャーナル: Mol Cell / 年: 2023
タイトル: Structural basis of a transcription pre-initiation complex on a divergent promoter.
著者: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami /
要旨: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
履歴
登録2022年3月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年3月1日Provider: repository / タイプ: Initial release
改定 1.12023年3月8日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.22024年6月12日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.initial_refinement_model_id

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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 (38-MER)
B: DNA (37-MER)
Ao: Mediator of RNA polymerase II transcription subunit 15
Ab: Mediator of RNA polymerase II transcription subunit 2
Ac: Mediator of RNA polymerase II transcription subunit 3
An: Mediator of RNA polymerase II transcription subunit 14
Ae: Mediator of RNA polymerase II transcription subunit 5
Ap: Mediator of RNA polymerase II transcription subunit 16
GA: Regulatory protein GAL4
GB: Regulatory protein GAL4
At: Mediator of RNA polymerase II transcription subunit 20
Ag: Mediator of RNA polymerase II transcription subunit 7
Ah: Mediator of RNA polymerase II transcription subunit 8
Ai: Mediator of RNA polymerase II transcription subunit 9
Aj: Mediator of RNA polymerase II transcription subunit 10
Ak: Mediator of RNA polymerase II transcription subunit 11
Aq: Mediator of RNA polymerase II transcription subunit 17
Ar: Mediator of RNA polymerase II transcription subunit 18
As: Mediator of RNA polymerase II transcription subunit 19
Au: Mediator of RNA polymerase II transcription subunit 21
Av: Mediator of RNA polymerase II transcription subunit 22
Aw: Mediator of RNA polymerase II transcription subunit 31
Az: DNA-directed RNA polymerase II subunit RPB1
AA: DNA-directed RNA polymerase II subunit RPB1
AB: DNA-directed RNA polymerase II subunit RPB2
AC: DNA-directed RNA polymerase II subunit RPB3
AD: DNA-directed RNA polymerase II subunit RPB4
AE: DNA-directed RNA polymerases I, II, and III subunit RPABC1
AF: DNA-directed RNA polymerases I, II, and III subunit RPABC2
AG: DNA-directed RNA polymerase II subunit RPB7
AH: DNA-directed RNA polymerases I, II, and III subunit RPABC3
AI: DNA-directed RNA polymerase II subunit RPB9
AJ: DNA-directed RNA polymerases I, II, and III subunit RPABC5
AK: DNA-directed RNA polymerase II subunit RPB11
AL: DNA-directed RNA polymerases I, II, and III subunit RPABC4
AM: Transcription initiation factor IIB
AP: Transcription initiation factor IIF subunit alpha
AQ: Transcription initiation factor IIF subunit beta
AS: Transcription elongation factor S-II
Aa: Mediator of RNA polymerase II transcription subunit 1
Ad: Mediator of RNA polymerase II transcription subunit 4
Af: Mediator of RNA polymerase II transcription subunit 6
Bo: Mediator of RNA polymerase II transcription subunit 15
Bb: Mediator of RNA polymerase II transcription subunit 2
Bc: Mediator of RNA polymerase II transcription subunit 3
Bn: Mediator of RNA polymerase II transcription subunit 14
Be: Mediator of RNA polymerase II transcription subunit 5
Bp: Mediator of RNA polymerase II transcription subunit 16
Bt: Mediator of RNA polymerase II transcription subunit 20
Bg: Mediator of RNA polymerase II transcription subunit 7
Bh: Mediator of RNA polymerase II transcription subunit 8
Bi: Mediator of RNA polymerase II transcription subunit 9
Bj: Mediator of RNA polymerase II transcription subunit 10
Bk: Mediator of RNA polymerase II transcription subunit 11
Bq: Mediator of RNA polymerase II transcription subunit 17
Br: Mediator of RNA polymerase II transcription subunit 18
Bs: Mediator of RNA polymerase II transcription subunit 19
Bu: Mediator of RNA polymerase II transcription subunit 21
Bv: Mediator of RNA polymerase II transcription subunit 22
Bw: Mediator of RNA polymerase II transcription subunit 31
Bz: DNA-directed RNA polymerase II subunit RPB1
BA: DNA-directed RNA polymerase II subunit RPB1
BB: DNA-directed RNA polymerase II subunit RPB2
BC: DNA-directed RNA polymerase II subunit RPB3
BD: DNA-directed RNA polymerase II subunit RPB4
BE: DNA-directed RNA polymerases I, II, and III subunit RPABC1
BF: DNA-directed RNA polymerases I, II, and III subunit RPABC2
BG: DNA-directed RNA polymerase II subunit RPB7
BH: DNA-directed RNA polymerases I, II, and III subunit RPABC3
BI: DNA-directed RNA polymerase II subunit RPB9
BJ: DNA-directed RNA polymerases I, II, and III subunit RPABC5
BK: DNA-directed RNA polymerase II subunit RPB11
BL: DNA-directed RNA polymerases I, II, and III subunit RPABC4
BM: Transcription initiation factor IIB
BP: Transcription initiation factor IIF subunit alpha
BQ: Transcription initiation factor IIF subunit beta
BS: Transcription elongation factor S-II
Ba: Mediator of RNA polymerase II transcription subunit 1
Bd: Mediator of RNA polymerase II transcription subunit 4
Bf: Mediator of RNA polymerase II transcription subunit 6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)3,456,48687
ポリマ－3,455,88380
非ポリマー6037
水00
1


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

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要素

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DNA鎖 , 2種, 2分子 AB

#1: DNA鎖 DNA (38-MER)


分子量: 11666.479 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Saccharomyces cerevisiae S288C (パン酵母)
#2: DNA鎖 DNA (37-MER)


分子量: 11424.310 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Saccharomyces cerevisiae S288C (パン酵母)

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Mediator of RNA polymerase II transcription subunit ... , 21種, 42分子 AoBoAbBbAcBcAnBnAeBeApBpAtBtAgBgAhBhAiBiAjBjAkBkAqBqArBrAsBs...

#3: タンパク質 Mediator of RNA polymerase II transcription subunit 15 / Autonomous replication regulatory protein 3 / Basal expression activator protein 1 / Defective ...Autonomous replication regulatory protein 3 / Basal expression activator protein 1 / Defective silencing suppressor protein 4 / Mediator complex subunit 15 / Transcription regulatory protein GAL11 / Ty insertion suppressor protein 13


分子量: 120432.242 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P19659
#4: タンパク質 Mediator of RNA polymerase II transcription subunit 2 / Mediator complex subunit 2


分子量: 47754.270 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: Q12124
#5: タンパク質 Mediator of RNA polymerase II transcription subunit 3 / Hyper-recombination suppressor protein 1 / Mediator complex subunit 3 / Poly-glutamine domain protein 1


分子量: 43116.039 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P40356
#6: タンパク質 Mediator of RNA polymerase II transcription subunit 14 / Glucose repression regulatory protein 1 / Mediator complex subunit 14


分子量: 123500.695 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P19263
#7: タンパク質 Mediator of RNA polymerase II transcription subunit 5 / Mediator complex subunit 5 / Negative regulator of URS2 protein 1


分子量: 128918.750 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P53114
#8: タンパク質 Mediator of RNA polymerase II transcription subunit 16 / Global transcriptional regulator SIN4 / Mediator complex subunit 16 / SNF1 suppressor protein 4 / ...Global transcriptional regulator SIN4 / Mediator complex subunit 16 / SNF1 suppressor protein 4 / SWI4 suppressor protein 5 / Transcriptional silencing factor 3 / YGP1 expression regulatory protein 1


分子量: 111423.422 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P32259
#10: タンパク質 Mediator of RNA polymerase II transcription subunit 20 / Hyper-recombination suppressor protein 2 / Mediator complex subunit 20 / Suppressor of RNA polymerase B 2


分子量: 22918.068 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P34162
#11: タンパク質 Mediator of RNA polymerase II transcription subunit 7 / Mediator complex subunit 7


分子量: 25616.062 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: Q08278
#12: タンパク質 Mediator of RNA polymerase II transcription subunit 8 / Mediator complex subunit 8


分子量: 25297.234 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P38304
#13: タンパク質 Mediator of RNA polymerase II transcription subunit 9 / Chromosome segregation protein 2 / Mediator complex subunit 9


分子量: 17400.377 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P33308
#14: タンパク質 Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10 / Negative regulator of URS2 protein 2


分子量: 17927.926 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: Q06213
#15: タンパク質 Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


分子量: 13324.189 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: Q99278
#16: タンパク質 Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17 / Suppressor of RNA polymerase B 4


分子量: 78582.836 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P32569
#17: タンパク質 Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / Suppressor of RNA polymerase B 5


分子量: 34316.539 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P32585
#18: タンパク質 Mediator of RNA polymerase II transcription subunit 19 / Hypoxic gene repressor protein 3 / Mediator complex subunit 19 / Negative regulator of URS2 protein ...Hypoxic gene repressor protein 3 / Mediator complex subunit 19 / Negative regulator of URS2 protein 3 / SNF1 suppressor protein 7


分子量: 24885.305 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P25046
#19: タンパク質 Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / RNAPII complex component SRB7 / Suppressor of RNA polymerase B 7


分子量: 16093.368 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P47822
#20: タンパク質 Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Suppressor of RNA polymerase B 6


分子量: 13774.628 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P32570
#21: タンパク質 Mediator of RNA polymerase II transcription subunit 31 / Hpr1 suppressor protein 1 / Mediator complex subunit 31


分子量: 14747.739 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P38633
#39: タンパク質 Mediator of RNA polymerase II transcription subunit 1 / Mediator complex subunit 1


分子量: 64314.953 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: Q12321
#40: タンパク質 Mediator of RNA polymerase II transcription subunit 4 / Mediator complex subunit 4


分子量: 32244.895 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: Q12343
#41: タンパク質 Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6


分子量: 32844.746 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P38782

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タンパク質 , 1種, 2分子 GAGB

#9: タンパク質 Regulatory protein GAL4


分子量: 16895.672 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: GAL4, YPL248C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P04386

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DNA-directed RNA polymerase II subunit ... , 8種, 16分子 AzBzAABAABBBACBCADBDAGBGAIBIAKBK

#22: タンパク質・ペプチド DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


分子量: 2611.681 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P04050, DNA-directed RNA polymerase
#23: タンパク質 DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


分子量: 162951.703 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P04050, DNA-directed RNA polymerase
#24: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


分子量: 138937.297 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P08518, DNA-directed RNA polymerase
#25: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


分子量: 35330.457 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P16370
#26: タンパク質 DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


分子量: 25451.191 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P20433
#29: タンパク質 DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


分子量: 19081.053 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P34087
#31: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


分子量: 14308.161 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P27999
#33: タンパク質 DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


分子量: 13633.493 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5種, 10分子 AEBEAFBFAHBHAJBJALBL

#27: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


分子量: 25117.094 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P20434
#28: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


分子量: 17931.834 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P20435
#30: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


分子量: 16525.363 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P20436
#32: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


分子量: 8290.732 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P22139
#34: 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


分子量: 7729.969 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P40422

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Transcription ... , 4種, 8分子 AMBMAPBPAQBQASBS

#35: タンパク質 Transcription initiation factor IIB / General transcription factor TFIIB / Transcription factor E


分子量: 38257.340 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P29055
#36: タンパク質 Transcription initiation factor IIF subunit alpha / TFIIF-alpha / TFIIF large subunit / Transcription factor G 105 kDa subunit / P105


分子量: 82320.570 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P41895
#37: タンパク質 Transcription initiation factor IIF subunit beta / ATP-dependent helicase TFG2 / TFIIF medium subunit / TFIIF-beta / Transcription factor G 54 kDa subunit


分子量: 46684.492 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae S288C (パン酵母)
参照: UniProt: P41896, DNA helicase
#38: タンパク質 Transcription elongation factor S-II / DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway ...DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway regulatory protein 2


分子量: 34903.551 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: DST1, PPR2, YGL043W / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P07273

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非ポリマー , 4種, 7分子

#42: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#43: 化合物 ChemComp-THR / THREONINE


タイプ: L-peptide linking / 分子量: 119.119 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H9NO3
#44: 化合物 ChemComp-ALA / ALANINE


タイプ: L-peptide linking / 分子量: 89.093 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H7NO2
#45: 化合物 ChemComp-ASP / ASPARTIC ACID


タイプ: L-peptide linking / 分子量: 133.103 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H7NO4

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詳細

研究の焦点であるリガンドがあるかY

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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: Med-PICearly / タイプ: COMPLEX / Entity ID: #1-#41 / 由来: MULTIPLE SOURCES
分子量実験値: NO
由来(天然)生物種: Saccharomyces cerevisiae S288C (パン酵母)
緩衝液pH: 7.6
試料濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドのタイプ: Quantifoil
急速凍結装置: LEICA EM CPC / 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: FEI TITAN KRIOS
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 / 倍率（公称値）: 64000 X / 倍率（補正後）: 64000 X / 最大 デフォーカス（公称値）: 3000 nm / 最小 デフォーカス（公称値）: 500 nm / Calibrated defocus min: 500 nm / 最大 デフォーカス（補正後）: 3000 nm / Cs: 2.7 mm
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影平均露光時間: 3.4 sec. / 電子線照射量: 42 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

EMソフトウェア
ID名称カテゴリ
7UCSF Chimeraモデルフィッティング
13PHENIX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: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 1102984 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT
原子モデル構築プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Cross-correlation
原子モデル構築
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameタイプ
17UI9

7ui9

17UI91PDBexperimental model
27UIL

7uil

17UIL2PDBexperimental model
37UIK

7uik

17UIK3PDBexperimental model

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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