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- PDB-7kts: Negative stain EM structure of the human SAGA coactivator complex... -

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基本情報

登録情報
データベース: PDB / ID: 7kts
タイトルNegative stain EM structure of the human SAGA coactivator complex (TRRAP, core, splicing module)
要素
  • (Splicing factor 3B subunit ...) x 2
  • (Transcription initiation factor TFIID subunit ...) x 3
  • Ataxin-7Ataxin 7
  • Isoform 3 of Transcription factor SPT20 homolog
  • STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma, DhaA
  • TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
  • TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L,TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L,TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
  • Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog転写 (生物学)
  • Transcriptional adapter 1
  • Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein
キーワードTRANSCRIPTION (転写 (生物学)) / splicing / gene regulation (遺伝子発現の調節) / chromatin (クロマチン)
機能・相同性
機能・相同性情報


regulation of macromolecule metabolic process / : / regulation of primary metabolic process / SAGA-type complex / positive regulation of response to stimulus / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / regulation of cellular response to stress ...regulation of macromolecule metabolic process / : / regulation of primary metabolic process / SAGA-type complex / positive regulation of response to stimulus / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / regulation of cellular response to stress / transcription factor TFTC complex / SLIK (SAGA-like) complex / splicing factor binding / U12-type spliceosomal complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / RNA polymerase binding / SAGA complex / U2 snRNP / limb development / 転写開始前複合体 / precatalytic spliceosome / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nucleus organization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / regulation of RNA splicing / histone deacetylase complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / U2 snRNA binding / regulation of DNA repair / somitogenesis / gastrulation / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / 視覚 / TBP-class protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / spliceosomal complex / mRNA transcription by RNA polymerase II / multicellular organism growth / negative regulation of protein catabolic process / G1/S transition of mitotic cell cycle / オートファジー / nuclear matrix / microtubule cytoskeleton organization / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / transcription corepressor activity / microtubule cytoskeleton / HATs acetylate histones / positive regulation of cell growth / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / nuclear speck / クロマチンリモデリング / protein heterodimerization activity / focal adhesion / apoptotic process / protein-containing complex binding / regulation of DNA-templated transcription / 核小体 / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / ゴルジ体 / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome
類似検索 - 分子機能
STAGA complex 65 subunit gamma / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Tra1, HEAT repeat ring region ...STAGA complex 65 subunit gamma / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Splicing factor 3B, subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40リピート / WD40リピート / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Transformation/transcription domain associated protein / Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 ...Transformation/transcription domain associated protein / Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Splicing factor 3B subunit 5 / Transcription initiation factor TFIID subunit 9B / TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
unclassified Rhodococcus (バクテリア)
手法電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 19.09 Å
データ登録者Herbst, D.A. / Esbin, M.N. / Nogales, E.
資金援助 米国, European Union, スイス, 6件
組織認可番号国
Howard Hughes Medical Institute (HHMI)CC30250 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127018 米国
European Molecular Biology Organization (EMBO)ALTF 1002-2018European Union
Swiss National Science FoundationP2BSP3_181878 スイス
Howard Hughes Medical Institute (HHMI)CC34430 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM098218 米国
引用ジャーナル: Nat Struct Mol Biol / 年: 2021
タイトル: Structure of the human SAGA coactivator complex.
著者: Dominik A Herbst / Meagan N Esbin / Robert K Louder / Claire Dugast-Darzacq / Gina M Dailey / Qianglin Fang / Xavier Darzacq / Robert Tjian / Eva Nogales /
要旨: The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are ...The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.
履歴
登録2020年11月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年11月10日Provider: repository / タイプ: Initial release
改定 1.12021年11月24日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name
改定 1.22021年12月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.32021年12月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.42024年5月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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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-23028
  • 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

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集合体

登録構造単位
A: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein
B: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
C: Isoform 3 of Transcription factor SPT20 homolog
D: STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma, DhaA
E: Transcription initiation factor TFIID subunit 9B
F: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L,TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L,TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
G: Transcription initiation factor TFIID subunit 12
H: Transcription initiation factor TFIID subunit 10
I: Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog
J: Transcriptional adapter 1
N: Ataxin-7
S: Splicing factor 3B subunit 3
T: Splicing factor 3B subunit 5


分子量 (理論値)分子数
合計 (水以外)1,100,24213
ポリマ－1,100,24213
非ポリマー00
水0
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
Buried area86410 Å2
ΔGint-527 kcal/mol
Surface area300440 Å2

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要素

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タンパク質 , 8種, 8分子 ABCDFIJN

#1: タンパク質 Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein


分子量: 419168.094 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: F2Z2U4
#2: タンパク質 TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / TAF5L / PCAF-associated factor 65 beta / PAF65-beta


分子量: 66223.047 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O75529
#3: タンパク質 Isoform 3 of Transcription factor SPT20 homolog / p38-interacting protein / p38IP


分子量: 88129.070 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8NEM7
#4: タンパク質 STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma, DhaA / Adenocarcinoma antigen ART1 / SPTF-associated factor 65 gamma / STAF65gamma / Suppressor of Ty 7-like


分子量: 83013.664 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Homo sapiens (ヒト), (組換発現) unclassified Rhodococcus (バクテリア)
遺伝子: SUPT7L, KIAA0764 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O94864
#6: タンパク質 TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L,TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L,TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L / TAF6L / PCAF-associated factor 65-alpha / PAF65-alpha


分子量: 62027.703 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y6J9
#9: タンパク質 Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog / 転写 (生物学) / SPT3-like protein


分子量: 35447.500 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O75486
#10: タンパク質 Transcriptional adapter 1 / SPT3-associated factor 42 / STAF42 / Transcriptional adapter 1-like protein


分子量: 37432.531 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96BN2
#11: タンパク質 Ataxin-7 / Ataxin 7 / Spinocerebellar ataxia type 7 protein


分子量: 95597.742 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O15265

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Transcription initiation factor TFIID subunit ... , 3種, 3分子 EGH

#5: タンパク質 Transcription initiation factor TFIID subunit 9B / Neuronal cell death-related protein 7 / DN-7 / Transcription initiation factor TFIID subunit 9-like ...Neuronal cell death-related protein 7 / DN-7 / Transcription initiation factor TFIID subunit 9-like / Transcription-associated factor TAFII31L


分子量: 27654.861 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9HBM6
#7: タンパク質 Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII20/TAFII15


分子量: 17948.467 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q16514
#8: タンパク質 Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAFII30


分子量: 21731.248 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q12962

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Splicing factor 3B subunit ... , 2種, 2分子 ST

#12: タンパク質 Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


分子量: 135718.844 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q15393
#13: タンパク質 Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


分子量: 10149.369 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9BWJ5

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詳細

配列の詳細Portions of chains A, D, F and I were not fully discernible in the map, and so many of the residues ...Portions of chains A, D, F and I were not fully discernible in the map, and so many of the residues were modeled as unknown (UNK) due to not knowing the register in these regions. The full sequence of the chains are as follows. Chain A: MAFVATQGATVVDQTTLMKKYLQFVAALTDVNTPDETKLKMMQEVSENFENVTSSPQYST FLEHIIPRFLTFLQDGEVQFLQEKPAQQLRKLVLEIIHRIPTNEHLRPHTKNVLSVMFRF LETENEENVLICLRIIIELHKQFRPPITQEIHHFLDFVKQIYKELPKVVNRYFENPQVIP ENTVPPPEMVGMITTIAVKVNPEREDSETRTHSIIPRGSLSLKVLAELPIIVVLMYQLYK LNIHNVVAEFVPLIMNTIAIQVSAQARQHKLYNKELYADFIAAQIKTLSFLAYIIRIYQE LVTKYSQQMVKGMLQLLSNCPAETAHLRKELLIAAKHILTTELRNQFIPCMDKLFDESIL IGSGYTARETLRPLAYSTLADLVHHVRQHLPLSDLSLAVQLFAKNIDDESLPSSIQTMSC KLLLNLVDCIRSKSEQESGNGRDVLMRMLEVFVLKFHTIARYQLSAIFKKCKPQSELGAV EAALPGVPTAPAAPGPAPSPAPVPAPPPPPPPPPPATPVTPAPVPPFEKQGEKDKEDKQT FQVTDCRSLVKTLVCGVKTITWGITSCKAPGAQFIPNKQLQPKETQIYIKLVKYAMQALD IYQVQIAGNGQTYIRVANCQTVRMKEEKEVLEHFAGVFTMMNPLTFKEIFQTTVPYMVER ISKNYALQIVANSFLANPTTSALFATILVEYLLDRLPEMGSNVELSNLYLKLFKLVFGSV SLFAAENEQMLKPHLHKIVNSSMELAQTAKEPYNYFLLLRALFRSIGGGSHDLLYQEFLP LLPNLLQGLNMLQSGLHKQHMKDLFVELCLTVPVRLSSLLPYLPMLMDPLVSALNGSQTL VSQGLRTLELCVDNLQPDFLYDHIQPVRAELMQALWRTLRNPADSISHVAYRVLGKFGGS NRKMLKESQKLHYVVTEVQGPSITVEFSDCKASLQLPMEKAIETALDCLKSANTEPYYRR QAWEVIKCFLVAMMSLEDNKHALYQLLAHPNFTEKTIPNVIISHRYKAQDTPARKTFEQA LTGAFMSAVIKDLRPSALPFVASLIRHYTMVAVAQQCGPFLLPCYQVGSQPSTAMFHSEE NGSKGMDPLVLIDAIAICMAYEEKELCKIGEVALAVIFDVASIILGSKERACQLPLFSYI VERLCACCYEQAWYAKLGGVVSIKFLMERLPLTWVLQNQQTFLKALLFVMMDLTGEVSNG AVAMAKTTLEQLLMRCATPLKDEERAEEIVAAQEKSFHHVTHDLVREVTSPNSTVRKQAM HSLQVLAQVTGKSVTVIMEPHKEVLQDMVPPKKHLLRHQPANAQIGLMEGNTFCTTLQPR LFTMDLNVVEHKVFYTELLNLCEAEDSALTKLPCYKSLPSLVPLRIAALNALAACNYLPQ SREKIIAALFKALNSTNSELQEAGEACMRKFLEGATIEVDQIHTHMRPLLMMLGDYRSLT LNVVNRLTSVTRLFPNSFNDKFCDQMMQHLRKWMEVVVITHKGGQRSDGNEMKICSAIIN LFHLIPAAPQTLVKPLLEVVMKTERAMLIEAGSPFREPLIKFLTRHPSQTVELFMMEATL NDPQWSRMFMSFLKHKDARPLRDVLAANPNRFITLLLPGGAQTAVRPGSPSTSTMRLDLQ FQAIKIISIIVKNDDSWLASQHSLVSQLRRVWVSENFQERHRKENMAATNWKEPKLLAYC LLNYCKRNYGDIELLFQLLRAFTGRFLCNMTFLKEYMEEEIPKNYSIAQKRALFFRFVDF NDPNFGDELKAKVLQHILNPAFLYSFEKGEGEQLLGPPNPEGDNPESITSVFITKVLDPE KQADMLDSLRIYLLQYATLLVEHAPHHIHDNNKNRNSKLRRLMTFAWPCLLSKACVDPAC KYSGHLLLAHIIAKFAIHKKIVLQVFHSLLKAHAMEARAIVRQAMAILTPAVPARMEDGH QMLTHWTRKIIVEEGHTVPQLVHILHLIVQHFKVYYPVRHHLVQHMVSAMQRLGFTPSVT IEQRRLAVDLSEVVIKWELQRIKDQQPDSDMDPNSSGEGVNSVSSSIKRGLSVDSAQEVK RFRTATGAISAVFGRSQSLPGADSLLAKPIDKQHTDTVVNFLIRVACQVNDNTNTAGSPG EVLSRRCVNLLKTALRPDMWPKSELKLQWFDKLLMTVEQPNQVNYGNICTGLEVLSFLLT VLQSPAILSSFKPLQRGIAACMTCGNTKVLRAVHSLLSRLMSIFPTEPSTSSVASKYEEL ECLYAAVGKVIYEGLTNYEKATNANPSQLFGTLMILKSACSNNPSYIDRLISVFMRSLQK MVREHLNPQAASGSTEATSAGTSELVMLSLELVKTRLAVMSMEMRKNFIQAILTSLIEKS PDAKILRAVVKIVEEWVKNNSPMAANQTPTLREKSILLVKMMTYIEKRFPEDLELNAQFL DLVNYVYRDETLSGSELTAKLEPAFLSGLRCAQPLIRAKFFEVFDNSMKRRVYERLLYVT CSQNWEAMGNHFWIKQCIELLLAVCEKSTPIGTSCQGAMLPSITNVINLADSHDRAAFAM VTHVKQEPRERENSESKEEDVEIDIELAPGDQTSTPKTKELSEKDIGNQLHMLTNRHDKF LDTLREVKTGALLSAFVQLCHISTTLAEKTWVQLFPRLWKILSDRQQHALAGEISPFLCS GSHQVQRDCQPSALNCFVEAMSQCVPPIPIRPCVLKYLGKTHNLWFRSTLMLEHQAFEKG LSLQIKPKQTTEFYEQESITPPQQEILDSLAELYSLLQEEDMWAGLWQKRCKYSETATAI AYEQHGFFEQAQESYEKAMDKAKKEHERSNASPAIFPEYQLWEDHWIRCSKELNQWEALT EYGQSKGHINPYLVLECAWRVSNWTAMKEALVQVEVSCPKEMAWKVNMYRGYLAICHPEE QQLSFIERLVEMASSLAIREWRRLPHVVSHVHTPLLQAAQQIIELQEAAQINAGLQPTNL GRNNSLHDMKTVVKTWRNRLPIVSDDLSHWSSIFMWRQHHYQAIVTAYENSSQHDPSSNN AMLGVHASASAIIQYGKIARKQGLVNVALDILSRIHTIPTVPIVDCFQKIRQQVKCYLQL AGVMGKNECMQGLEVIESTNLKYFTKEMTAEFYALKGMFLAQINKSEEANKAFSAAVQMH DVLVKAWAMWGDYLENIFVKERQLHLGVSAITCYLHACRHQNESKSRKYLAKVLWLLSFD DDKNTLADAVDKYCIGVPPIQWLAWIPQLLTCLVGSEGKLLLNLISQVGRVYPQAVYFPI RTLYLTLKIEQRERYKSDSGQQQPSSVGNQSHSASDPGPIRATAPMWRCSRIMHMQRELH PTLLSSLEGIVDQMVWFRENWHEEVLRQLQQGLAKCYSVAFEKSGAVSDAKITPHTLNFV KKLVSTFGVGLENVSNVSTMFSSAASESLARRAQATAQDPVFQKLKGQFTTDFDFSVPGS MKLHNLISKLKKWIKILEAKTKQLPKFFLIEEKCRFLSNFSAQTAEVEIPGEFLMPKPTH YYIKIARFMPRVEIVQKHNTAARRLYIRGHNGKIYPYLVMNDACLTESRREERVLQLLRL LNPCLEKRKETTKRHLFFTVPRVVAVSPQMRLVEDNPSSLSLVEIYKQRCAKKGIEHDNP ISRYYDRLATVQARGTQASHQVLRDILKEVQSNMVPRSMLKEWALHTFPNATDYWTFRKM FTIQLALIGFAEFVLHLNRLNPEMLQIAQDTGKLNVAYFRFDINDATGDLDANRPVPFRL TPNISEFLTTIGVSGPLTASMIAVARCFAQPNFKVDGILKTVLRDEIIAWHKKTQEDTSS PLSAAGQPENMDSQQLVSLVQKAVTAIMTRLHNLAQFEGGESKVNTLVAAANSLDNLCRM DPAWHPWL Chain D: MNLQRYWGEIPISSSQTNRSSFDLLPREFRLVEVHDPPLHQPSANKPKPPTMLDIPSEPC SLTIHTIQLIQHNRRLRNLIATAQAQNQQQTEGVKTEESEPLPSCPGSPPLPDDLLPLDC KNPNAPFQIRHSDPESDFYRGKGEPVTELSWHSCRQLLYQAVATILAHAGFDCANESVLE TLTDVAHEYCLKFTKLLRFAVDREARLGQTPFPDVMEQVFHEVGIGSVLSLQKFWQHRIK DYHSYMLQISKQLSEEYERIVNPEKATEDAKPVKIKEEPVSDITFPVSEELEADLASGDQ SLPMGVLGAQSERFPSNLEVEASPQASSAEVNASPLWNLAHVKMEPQESEEGNVSGHGVL GSDVFEEPMSGMSEAGIPQSPDDSDSSYGSHSTDSLMGSSPVFNQRCKKRMRKIGTSGED LYFQSGGSMAEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNII PHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALG FHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGT LPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQS PVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLST LEISGDYKDHDGDYKDHDIDYKDDDDKGS Chain F: MSEREERRFVEIPRESVRLMAESTGLELSDEVAALLAEDVCYRLREATQNSSQFMKHTKR RKLTVEDFNRALRWSSVEAVCGYGSQEALPMRPAREGELYFPEDREVNLVELALATNIPK GCAETAVRVHVSYLDGKGNLAPQGSVPSAVSSLTDDLLKYYHQVTRAVLGDDPQLMKVAL QDLQTNSKIGALLPYFVYVVSGVKSVSHDLEQLHRLLQVARSLFRNPHLCLGPYVRCLVG SVLYCVLEPLAASINPLNDHWTLRDGAALLLSHIFWTHGDLVSGLYQHILLSLQKILADP VRPLCCHYGAVVGLHALGWKAVERVLYPHLSTYWTNLQAVLDDYSVSNAQVKADGHKVYG AILVAVERLLKMKAQAAEPNRGGPGGRGCRRLDDLPWDSLLFQESSSGGGAEPSFGSGLP LPPGGAGPEDPSLSVTLADIYRELYAFFGDSLATRFGTGQPAPTAPRPPGDKKEPAAAPD SVRKMPQLTASAIVSPHGDESPRGSGGGGPASASGPAASESRPLPRVHRARGAPRQQGPG TGTRDVFQKSRFAPRGAPHFRFIIAGRQAGRRCRGRLFQTAFPAPYGPSPASRYVQKLPM IGRTSRPARRWALSDYSLYLPL Chain I: MNNTAASPMSTATSSSGRSTGKSISFATELQSMMYSLGDARRPLHETAVLVEDVVHTQLI NLLQQAAEVSQLRGARVITPEDLLFLMRKDKKKLRRLLKYMFIRDYKSKIVKGIDEDDLL EDKLSGSNNANKRQKIAQDFLNSIDQTGELLAMFEDDEIDEVKQERMERAERQTRIMDSA QYAEFCESRQLSFSKKASKFRDWLDCSSMEIKPNVVAMEILAYLAYETVAQLVDLALLVR QDMVTKAGDPFSHAISATFIQYHNSAESTAACGVEAHSDAIQPCHIREAIRRYSHRIGPL SPFTNAYRRNGMAFLAC

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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
ID名称タイプ詳細Entity IDParent-ID由来
1human SAGACOMPLEXendogeneous human SAGA purified from HeLa cellsall0MULTIPLE SOURCES
2human SAGACOMPLEXendogeneous human SAGA purified from HeLa cells#1-#3, #5-#131NATURAL
3STAGA complex 65 subunit gammaCOMPLEX#41RECOMBINANT
分子量値: 1.420272 MDa / 実験値: NO
由来(天然)
IDEntity assembly-ID生物種Ncbi tax-ID株組織
12Homo sapiens (ヒト)9606HeLacervix
23Homo sapiens (ヒト)9606HeLacervix
33unclassified Rhodococcus (バクテリア)192944
由来(組換発現)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.5 / 詳細: Buffers were freshly prepared and 0.22 um filtered.
緩衝液成分
ID濃度名称式Buffer-ID
125 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
2200 mMsodium chloride塩化ナトリウムNaCl塩化ナトリウム1
30.2 mMEthylenediaminetetraacetic acidエチレンジアミン四酢酸1
46 mMmagnesium chlorideMgCl21
53 % (w/v)D(+)trehalose1
試料包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO
詳細: The sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing
染色タイプ: NEGATIVE / 染色剤: uranyl formate
試料支持グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Homemade

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電子顕微鏡撮影

顕微鏡モデル: FEI TECNAI 20
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 120 kV / 照射モード: SPOT SCAN
電子レンズモード: BRIGHT FIELDBright-field microscopy / 倍率（公称値）: 80000 X / 最大 デフォーカス（公称値）: 3900 nm / 最小 デフォーカス（公称値）: 400 nm / Cs: 2.2 mm / アライメント法: BASIC
試料ホルダ試料ホルダーモデル: SIDE ENTRY, EUCENTRIC
撮影電子線照射量: 35 e/Å2
フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k)
撮影したグリッド数: 1 / 実像数: 745

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解析

ソフトウェア名称: PHENIX / バージョン: 1.18.2_3874: / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ
2Leginon画像取得
4CTFFIND4.7.0CTF補正
7Coot0.8.9.2モデルフィッティング
9RELION3.1初期オイラー角割当
10RELION3.1最終オイラー角割当
11RELION3.1分類
12RELION3.1３次元再構成
13PHENIX1.18.2-3874モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 45790
3次元再構成解像度: 19.09 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 3157 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 3 / 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
原子モデル構築

3D fitting-ID: 1 / Accession code: 5IFE / Initial refinement model-ID: 1 / PDB-ID: 5IFE

5ife

/ Source name: PDB / タイプ: experimental model

IDPDB chain-IDPdb chain residue range
1B15-80
2A1-1217
精密化詳細: No high-resolution structure of the TAF6L HEAT domain (F154-F374) is available. A homology model for this region (based on PDB 6MZL) was generated using SwissModel. To reflect the model ...詳細: No high-resolution structure of the TAF6L HEAT domain (F154-F374) is available. A homology model for this region (based on PDB 6MZL) was generated using SwissModel. To reflect the model uncertainty it was deposited as UNKs

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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