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- PDB-8t9d: CryoEM structure of TR-TRAP -

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基本情報

登録情報
データベース: PDB / ID: 8t9d
タイトルCryoEM structure of TR-TRAP
要素
  • (Mediator of RNA polymerase II transcription subunit ...) x 25
  • Unknown Peptide
キーワードSTRUCTURAL PROTEIN / TR-TRAP / mediator / CKM module
機能・相同性
機能・相同性情報


positive regulation of mediator complex assembly / positive regulation of T cell extravasation / CKM complex / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / CKM complex / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / triglyceride homeostasis / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / positive regulation of chromatin binding / limb development / lens development in camera-type eye / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / megakaryocyte development / histone acetyltransferase binding / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / cortical actin cytoskeleton / termination of RNA polymerase II transcription / RSV-host interactions / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / fat cell differentiation / skeletal muscle cell differentiation / mammary gland branching involved in pregnancy / somatic stem cell population maintenance / monocyte differentiation / blastocyst development / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of fibroblast proliferation / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / liver development / cholesterol homeostasis / promoter-specific chromatin binding / nuclear estrogen receptor binding / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / brain development / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / transcription coactivator binding / DNA-directed 5'-3' RNA polymerase activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / Circadian Clock / actin binding / angiogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression
類似検索 - 分子機能
MID domain of medPIWI / MID domain of medPIWI / Mediator complex subunit Med13, C-terminal / Mediator complex subunit 13 C-terminal domain / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 ...MID domain of medPIWI / MID domain of medPIWI / Mediator complex subunit Med13, C-terminal / Mediator complex subunit 13 C-terminal domain / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 / Mediator complex subunit 25 von Willebrand factor type A / Mediator complex, subunit Med29, metazoa / Mediator complex, subunit Med24, / : / Mediator complex subunit 24 N-terminal / Mediator complex subunit 29 / Mediator complex subunit 16, central helical bridge / Mediator complex, subunit Med23 / Mediator complex subunit 23 / Mediator of RNA polymerase II transcription subunit 15 / : / : / ARC105/Med15 mediator subunit N-terminal KIX domain / ARC105/Med15 mediator subunit central domain / ARC105/Med15 mediator subunit C-terminal domain / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med28 / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator complex subunit 30 / Mediator complex subunit 28 / Mediator complex, subunit Med27 / Mediator complex subunit 27 / : / : / 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 / Mediator complex, subunit Med7 superfmaily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / 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 / Soluble quinoprotein glucose/sorbosone dehydrogenase / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / 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 / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Coactivator CBP, KIX domain superfamily / von Willebrand factor A-like domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 25 / Mediator of RNA polymerase II transcription subunit 8 ...Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 25 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 30 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 29 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 13 / Mediator of RNA polymerase II transcription subunit 23 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 31
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: 4.66 Å
データ登録者Zhao, H. / Asturias, F.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-67167 米国
引用ジャーナル: Mol Cell / 年: 2024
タイトル: An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II.
著者: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / Srinivas ...著者: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / Srinivas Ramachandran / Robert G Roeder / Yi Shi / Rafael Casellas / Francisco J Asturias /
要旨: The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent ...The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
履歴
登録2023年6月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年7月3日Provider: repository / タイプ: Initial release
改定 1.12024年7月17日Group: Data collection / Database references / カテゴリ: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: Mediator of RNA polymerase II transcription subunit 1
B: Mediator of RNA polymerase II transcription subunit 4
C: Mediator of RNA polymerase II transcription subunit 6
D: Mediator of RNA polymerase II transcription subunit 7
E: Mediator of RNA polymerase II transcription subunit 8
F: Mediator of RNA polymerase II transcription subunit 9
G: Mediator of RNA polymerase II transcription subunit 10
H: Mediator of RNA polymerase II transcription subunit 11
I: Mediator of RNA polymerase II transcription subunit 14
J: Mediator of RNA polymerase II transcription subunit 15
K: Mediator of RNA polymerase II transcription subunit 16
L: Mediator of RNA polymerase II transcription subunit 17
M: Mediator of RNA polymerase II transcription subunit 18
O: Mediator of RNA polymerase II transcription subunit 20
P: Mediator of RNA polymerase II transcription subunit 21
Q: Mediator of RNA polymerase II transcription subunit 22
R: Mediator of RNA polymerase II transcription subunit 23
S: Mediator of RNA polymerase II transcription subunit 24
T: Mediator of RNA polymerase II transcription subunit 25
V: Mediator of RNA polymerase II transcription subunit 27
W: Mediator of RNA polymerase II transcription subunit 28
X: Mediator of RNA polymerase II transcription subunit 29
Y: Mediator of RNA polymerase II transcription subunit 30
Z: Mediator of RNA polymerase II transcription subunit 31
a: Unknown Peptide
9: Mediator of RNA polymerase II transcription subunit 13


分子量 (理論値)分子数
合計 (水以外)1,529,69226
ポリマ－1,529,69226
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_555x,y,z1

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要素

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Mediator of RNA polymerase II transcription subunit ... , 25種, 25分子 ABCDEFGHIJKLMOPQRSTVWXYZ9

#1: タンパク質 Mediator of RNA polymerase II transcription subunit 1 / Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome ...Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TR-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


分子量: 168697.328 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA / 参照: UniProt: Q15648
#2: タンパク質 Mediator of RNA polymerase II transcription subunit 4 / Activator-recruited cofactor 36 kDa component / ARC36 / Mediator complex subunit 4 / TRAP/SMCC/PC2 ...Activator-recruited cofactor 36 kDa component / ARC36 / Mediator complex subunit 4 / TRAP/SMCC/PC2 subunit p36 subunit / Vitamin D3 receptor-interacting protein complex 36 kDa component / DRIP36


分子量: 29781.424 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA / 参照: UniProt: Q9NPJ6
#3: タンパク質 Mediator of RNA polymerase II transcription subunit 6 / Activator-recruited cofactor 33 kDa component / ARC33 / Mediator complex subunit 6 / hMed6 / Renal ...Activator-recruited cofactor 33 kDa component / ARC33 / Mediator complex subunit 6 / hMed6 / Renal carcinoma antigen NY-REN-28


分子量: 28464.627 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA / 参照: UniProt: O75586
#4: タンパク質 Mediator of RNA polymerase II transcription subunit 7 / hMED7 / Activator-recruited cofactor 34 kDa component / ARC34 / Cofactor required for Sp1 ...hMED7 / Activator-recruited cofactor 34 kDa component / ARC34 / Cofactor required for Sp1 transcriptional activation subunit 9 / CRSP complex subunit 9 / Mediator complex subunit 7 / RNA polymerase transcriptional regulation mediator subunit 7 homolog / Transcriptional coactivator CRSP33


分子量: 27285.281 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O43513
#5: タンパク質 Mediator of RNA polymerase II transcription subunit 8 / Activator-recruited cofactor 32 kDa component / ARC32 / Mediator complex subunit 8


分子量: 29112.906 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96G25
#6: タンパク質 Mediator of RNA polymerase II transcription subunit 9 / Mediator complex subunit 9


分子量: 16422.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9NWA0
#7: タンパク質 Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10 / Transformation-related gene 17 protein / TRG-17 / Transformation- ...Mediator complex subunit 10 / Transformation-related gene 17 protein / TRG-17 / Transformation-related gene 20 protein / TRG-20


分子量: 15710.969 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9BTT4
#8: タンパク質 Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


分子量: 13145.829 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9P086
#9: タンパク質 Mediator of RNA polymerase II transcription subunit 14 / Activator-recruited cofactor 150 kDa component / ARC150 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 150 kDa component / ARC150 / Cofactor required for Sp1 transcriptional activation subunit 2 / CRSP complex subunit 2 / Mediator complex subunit 14 / RGR1 homolog / hRGR1 / Thyroid hormone receptor-associated protein complex 170 kDa component / Trap170 / Transcriptional coactivator CRSP150 / Vitamin D3 receptor-interacting protein complex 150 kDa component / DRIP150


分子量: 160787.594 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O60244
#10: タンパク質 Mediator of RNA polymerase II transcription subunit 15 / Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex ...Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex subunit 15 / Positive cofactor 2 glutamine/Q-rich-associated protein / PC2 glutamine/Q-rich-associated protein / TPA-inducible gene 1 protein / TIG-1 / Trinucleotide repeat-containing gene 7 protein


分子量: 86830.102 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96RN5
#11: タンパク質 Mediator of RNA polymerase II transcription subunit 16 / Mediator complex subunit 16 / Thyroid hormone receptor-associated protein 5 / Thyroid hormone ...Mediator complex subunit 16 / Thyroid hormone receptor-associated protein 5 / Thyroid hormone receptor-associated protein complex 95 kDa component / Trap95 / Vitamin D3 receptor-interacting protein complex 92 kDa component / DRIP92


分子量: 96908.055 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y2X0
#12: タンパク質 Mediator of RNA polymerase II transcription subunit 17 / Activator-recruited cofactor 77 kDa component / ARC77 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 77 kDa component / ARC77 / Cofactor required for Sp1 transcriptional activation subunit 6 / CRSP complex subunit 6 / Mediator complex subunit 17 / Thyroid hormone receptor-associated protein complex 80 kDa component / Trap80 / Transcriptional coactivator CRSP77 / Vitamin D3 receptor-interacting protein complex 80 kDa component / DRIP80


分子量: 72984.047 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9NVC6
#13: タンパク質 Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / p28b


分子量: 23693.730 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9BUE0
#14: タンパク質 Mediator of RNA polymerase II transcription subunit 20 / Mediator complex subunit 20 / TRF-proximal protein homolog / hTRFP


分子量: 23243.762 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9H944
#15: タンパク質 Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex ...Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex component SRB7 / hSrb7


分子量: 15575.234 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q13503
#16: タンパク質 Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Surfeit locus protein 5 / Surf-5


分子量: 22243.713 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q15528
#17: タンパク質 Mediator of RNA polymerase II transcription subunit 23 / Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional activation subunit 3 / CRSP complex subunit 3 / Mediator complex subunit 23 / Protein sur-2 homolog / hSur-2 / Transcriptional coactivator CRSP130 / Vitamin D3 receptor-interacting protein complex 130 kDa component / DRIP130


分子量: 156652.156 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9ULK4
#18: タンパク質 Mediator of RNA polymerase II transcription subunit 24 / Activator-recruited cofactor 100 kDa component / ARC100 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 100 kDa component / ARC100 / Cofactor required for Sp1 transcriptional activation subunit 4 / CRSP complex subunit 4 / Mediator complex subunit 24 / Thyroid hormone receptor-associated protein 4 / Thyroid hormone receptor-associated protein complex 100 kDa component / Trap100 / hTRAP100 / Vitamin D3 receptor-interacting protein complex 100 kDa component / DRIP100


分子量: 110430.164 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O75448
#19: タンパク質 Mediator of RNA polymerase II transcription subunit 25 / Activator interaction domain-containing protein 1 / Activator-recruited cofactor 92 kDa component / ...Activator interaction domain-containing protein 1 / Activator-recruited cofactor 92 kDa component / ARC92 / Mediator complex subunit 25 / p78


分子量: 78230.344 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q71SY5
#20: タンパク質 Mediator of RNA polymerase II transcription subunit 27 / Cofactor required for Sp1 transcriptional activation subunit 8 / CRSP complex subunit 8 / Mediator ...Cofactor required for Sp1 transcriptional activation subunit 8 / CRSP complex subunit 8 / Mediator complex subunit 27 / P37 TRAP/SMCC/PC2 subunit / Transcriptional coactivator CRSP34


分子量: 35478.742 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q6P2C8
#21: タンパク質 Mediator of RNA polymerase II transcription subunit 28 / Endothelial-derived protein 1 / Mediator complex subunit 28 / Merlin and Grb2-interacting ...Endothelial-derived protein 1 / Mediator complex subunit 28 / Merlin and Grb2-interacting cytoskeletal protein / Magicin / Tumor angiogenesis marker EG-1


分子量: 19540.107 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9H204
#22: タンパク質 Mediator of RNA polymerase II transcription subunit 29 / Intersex-like protein / Mediator complex subunit 29


分子量: 21089.801 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9NX70
#23: タンパク質 Mediator of RNA polymerase II transcription subunit 30 / Mediator complex subunit 30 / TRAP/Mediator complex component TRAP25 / Thyroid hormone receptor- ...Mediator complex subunit 30 / TRAP/Mediator complex component TRAP25 / Thyroid hormone receptor-associated protein 6 / Thyroid hormone receptor-associated protein complex 25 kDa component / Trap25


分子量: 20301.229 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96HR3
#24: タンパク質 Mediator of RNA polymerase II transcription subunit 31 / Mediator complex subunit 31 / Mediator complex subunit SOH1 / hSOH1


分子量: 15826.116 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y3C7
#26: タンパク質 Mediator of RNA polymerase II transcription subunit 13 / Activator-recruited cofactor 250 kDa component / ARC250 / Mediator complex subunit 13 / Thyroid ...Activator-recruited cofactor 250 kDa component / ARC250 / Mediator complex subunit 13 / Thyroid hormone receptor-associated protein 1 / Thyroid hormone receptor-associated protein complex 240 kDa component / Trap240 / Vitamin D3 receptor-interacting protein complex component DRIP250 / DRIP250


分子量: 239535.906 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9UHV7

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タンパク質・ペプチド , 1種, 1分子 a

#25: タンパク質・ペプチド Unknown Peptide


分子量: 1720.111 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト)

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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: mediator complex with transcription factor TR / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL
由来(天然)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.9
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: Talos Arctica / 画像提供: FEI Company
顕微鏡モデル: FEI TECNAI ARCTICA
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 35000 nm / 最小 デフォーカス（公称値）: 800 nm
撮影電子線照射量: 100 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

CTF補正タイプ: NONE
3次元再構成解像度: 4.66 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 31505 / 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://pdbjlvh1.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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