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- PDB-7ktr: Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) -

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基本情報

登録情報
データベース: PDB / ID: 7ktr
タイトルCryo-EM structure of the human SAGA coactivator complex (TRRAP, core)
要素
  • (Transcription initiation factor TFIID subunit ...) x 3
  • Ataxin-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
  • Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog
  • Transcriptional adapter 1
  • 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 / coactivator / gene regulation / chromatin
機能・相同性
機能・相同性情報


SAGA-type complex / 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 / negative regulation of microtubule depolymerization / hepatocyte differentiation ...SAGA-type complex / 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 / negative regulation of microtubule depolymerization / hepatocyte differentiation / maintenance of protein location in nucleus / RNA polymerase binding / limb development / SAGA complex / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / transcription factor TFIID complex / 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 / histone deacetylase complex / regulation of RNA splicing / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / gastrulation / visual perception / TBP-class protein binding / nuclear estrogen receptor binding / transcription coregulator activity / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / G1/S transition of mitotic cell cycle / autophagy / microtubule cytoskeleton organization / multicellular organism growth / nuclear matrix / cytoplasmic ribonucleoprotein granule / transcription corepressor activity / HATs acetylate histones / microtubule cytoskeleton / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / Ub-specific processing proteases / protein stabilization / nuclear speck / chromatin remodeling / protein heterodimerization activity / focal adhesion / apoptotic process / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
TFIID subunit TAF5, NTD2 domain / STAGA complex 65 subunit gamma / : / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SCA7 domain / SCA7, zinc-binding domain ...TFIID subunit TAF5, NTD2 domain / STAGA complex 65 subunit gamma / : / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / 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 / Transcription initiation factor IID, 31kD subunit / Bromodomain transcription factors and PHD domain containing proteins / Transcription initiation factor TAFII31 / Bromodomain associated / Bromodomain associated domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / : / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Histone-fold / Armadillo-like helical / Alpha Horseshoe / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Alpha
類似検索 - ドメイン・相同性
INOSITOL HEXAKISPHOSPHATE / 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 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 ...INOSITOL HEXAKISPHOSPHATE / 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 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / 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 / クライオ電子顕微鏡法 / 解像度: 2.93 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 / カテゴリ: chem_comp_atom / chem_comp_bond

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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-23027
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: 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
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)887,72812
ポリマ－887,06811
非ポリマー6601
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
Buried area82400 Å2
ΔGint-510 kcal/mol
Surface area236220 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 / TRRAP


分子量: 353170.281 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 / SUPT20H


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- ...Adenocarcinoma antigen ART1 / SPTF-associated factor 65 gamma / STAF65gamma / Suppressor of Ty 7-like / SUPT7L / Adenocarcinoma antigen ART1 / SPTF-associated factor 65 gamma / STAF65gamma / Suppressor of Ty 7-like


分子量: 78079.922 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 / TAF6L / PCAF-associated factor 65-alpha / PAF65-alpha


分子量: 67903.289 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 / SPT3-like protein / SUPT3H / SPT3-like protein


分子量: 33197.047 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 / 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 / TAF9B


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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非ポリマー , 1種, 1分子

#12: 化合物 ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / myo-イノシト-ル六りん酸


分子量: 660.035 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H18O24P6 / タイプ: SUBJECT OF INVESTIGATION

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詳細

研究の焦点であるリガンドがあるかY
配列の詳細Portions of chains A, D and I were not fully discernible in the map, and so many of the residues ...Portions of chains A, D 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 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 cells#1-#110MULTIPLE SOURCES
2human SAGACOMPLEXendogeneous human SAGA purified from HeLa cells#1-#3, #5-#111NATURAL
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
22Homo sapiens (ヒト)9606HeLacervix
33Homo sapiens (ヒト)9606
43unclassified Rhodococcus (バクテリア)192944
由来(組換発現)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.8 / 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 chlorideNaCl1
30.2 mMEthylenediaminetetraacetic acid1
40.5 mMtris(2-carboxyethyl)phosphine1
50.01 % (v/v)nonyl phenoxypolyethoxylethanol1
62.5 % (v/v)Glycerol1
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
詳細: The sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing
試料支持グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: UltrAuFoil R1.2/1.3
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K / 詳細: blot force 0, blot time 3 sec

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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: SPOT SCAN
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 64000 X / 最大 デフォーカス（公称値）: 3400 nm / 最小 デフォーカス（公称値）: 900 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 50 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)
撮影したグリッド数: 1 / 実像数: 10224
電子光学装置エネルギーフィルター名称: GIF Bioquantum

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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
2SerialEM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: 2438694
3次元再構成解像度: 2.93 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 209435 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 2 / 対称性のタイプ: POINT
原子モデル構築プロトコル: AB INITIO MODEL / 空間: REAL
精密化詳細: Residues for which the register could not be unambiguously assigned were modeled as UNKs. Additional density corresponding to the linkers I259-I277 and J232-J247 can be observed at the ...詳細: Residues for which the register could not be unambiguously assigned were modeled as UNKs. Additional density corresponding to the linkers I259-I277 and J232-J247 can be observed at the interface between the core and TRRAP module, but could not be clearly assigned to one of the subunits. Connected loop density is observed but not modeled due to insufficient information on register, linker length, or confidence in backbone assignment: A1689-A1692, A1722-A1728, A1769-A1786, A1800-1805, A1823-A1837, A2181-A2192, A2209-A2217, A2239-A2248, A2291-A2299, C27-C30 Density corresponding to H182-H187 is observed, might be explained by multiple main chain conformations and was not modeled. Continuous density for linkers connecting an unassigned (UNK) with an assigned region, corresponding to D48-D51 and D118, is observed but was omitted, because the register in the unassigned (UNK) regions could not be assigned. Region I174-I185 and its connection is observed in the LocSpiral (Kaur, S. et al., bioRxiv 2020) filtered multibody maps. The cis-peptide bond of A3698 is defined by coulomb density. Mass spectrometry did not distinguish between the isoforms (uniprot) Q8NEM7-2 and Q8NEM7-3 of SUPT20H (chain C). Both isoforms distinguish primarily in disordered regions. In an ordered region, Q8NEM7-2 and Q8NEM7-3 distinguish by an insertion of one amino acid (Gln56 in Q8NEM7-2), which is better explained by Q8NEM7-3. Mass spectrometry did not distinguish between the isoforms (uniprot) O94864 and O94864-2 (chain D). Both isoforms distinguish by two N-terminal amino acids in a disordered region. The sequence numbering corresponds to O94864. Mass spectrometry indicated that (uniprot) Q9HBM6 (TAF9B) and Q16594 (TAF9) were present in the sample. TAF9B explains the density slightly better (chain E), however, it is possible that both subunits are present in the complex. Mass spectrometry did not distinguish between the isoforms (uniprot) Q16514 and Q16514-2 (chain G). Both isoforms distinguish in the disordered N-terminus. Due to a 5x higher abundance of Q16514 in all cell types and the requirement of the longer N-terminal domain for transcriptional activation (Hamard, P.-J., et al. Oncogene. 2005 May 12;24(21):3472-83.), Q16514 was modeled. Mass spectrometry indicated that (uniprot) O15265 (ATXN7), Q9ULK2 (ATXN7L1), and Q5T6C5 (ATXN7L2) were present in the sample. The density is explained best by ATXN7 and ATXN7L1 (in this order) (chain N), however, it is possible that a mixture of all subunits is present. The modeled isoforms of all other subunits were determined either by mass spectrometry or density fit. The ligand INOSITOL HEXAKISPHOSPHATE (IHP) was identified by density fit and homology to mTORC2 (PDB 6ZWO, Scaliola A., et al. Sci Adv. 2020 Nov 6;6(45)). Additional density close to P4 might be explained by an alternative conformation or an ordered water molecule. Only the conformation with the better geometry was modeled.
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.00441124
ELECTRON MICROSCOPYf_angle_d0.53755737
ELECTRON MICROSCOPYf_dihedral_angle_d10.1475569
ELECTRON MICROSCOPYf_chiral_restr0.0366361
ELECTRON MICROSCOPYf_plane_restr0.0047167

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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