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- EMDB-23027: Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) -

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IDまたはキーワード:

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基本情報

登録情報
データベース: EMDB / ID: EMD-23027
タイトルCryo-EM structure of the human SAGA coactivator complex (TRRAP, core)
マップデータLocSpiral filtered map
試料
  • 複合体: human SAGA
    • 複合体: human SAGA
      • タンパク質・ペプチド: x 10種
    • 複合体: STAGA complex 65 subunit gamma
      • タンパク質・ペプチド: x 1種
  • リガンド: x 1種
キーワードcoactivator / gene regulation / transcription / chromatin
機能・相同性
機能・相同性情報


SAGA-type complex / positive regulation of response to stimulus / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization ...SAGA-type complex / positive regulation of response to stimulus / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / maintenance of protein location in nucleus / RNA polymerase binding / SAGA complex / limb development / transcription preinitiation complex / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / NuA4 histone acetyltransferase 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 / regulation of RNA splicing / histone deacetylase complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / somitogenesis / RNA polymerase II preinitiation complex assembly / gastrulation / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / 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 / mRNA transcription by RNA polymerase II / multicellular organism growth / autophagy / cytoplasmic ribonucleoprotein granule / nuclear matrix / microtubule cytoskeleton organization / G1/S transition of mitotic cell cycle / 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 / chromatin remodeling / protein heterodimerization activity / DNA repair / focal adhesion / apoptotic process / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / 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 / 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 / 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 repeats / WD40 repeat / 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 / 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 DA / Esbin MN
資金援助 米国, European Union, スイス, 6件
OrganizationGrant number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-
ヘッダ(付随情報) 公開2021年11月10日-
マップ公開2021年11月10日-
更新2024年5月29日-
現状2024年5月29日処理サイト: RCSB / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 6.37
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（半径に従い着色）
  • 表面レベル: 6.37
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-7ktr
  • 表面レベル: 6.37
  • 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EMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_23027.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_23027.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈LocSpiral filtered map
ボクセルのサイズX=Y=Z: 1.187 Å
密度
表面レベル登録者による: 6.37 / ムービー #1: 6.37
最小 - 最大0.0 - 25.375306999999999
平均 (標準偏差)0.17207587 (±0.75278217)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ360360360
Spacing360360360
セルA=B=C: 427.32 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.1871.1871.187
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z427.320427.320427.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean0.00025.3750.172

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添付データ

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マスク #1

ファイルemd_23027_msk_1.map
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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追加マップ: LocSpiral filtered multibody map of the TRRAP module

ファイルemd_23027_additional_1.map
注釈LocSpiral filtered multibody map of the TRRAP module
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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追加マップ: LocSpiral filtered multibody map of the core module

ファイルemd_23027_additional_2.map
注釈LocSpiral filtered multibody map of the core module
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

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追加マップ: Relion postprocessed map

ファイルemd_23027_additional_3.map
注釈Relion postprocessed map
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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ハーフマップ: half map 2

ファイルemd_23027_half_map_1.map
注釈half map 2
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

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ヒストグラム (対数)

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ハーフマップ: half map 1

ファイルemd_23027_half_map_2.map
注釈half map 1
投影像・断面図
軸ZYX

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断面 (1/2)
密度ヒストグラム

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試料の構成要素

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全体 : human SAGA

全体名称: human SAGA
要素
  • 複合体: human SAGA
    • 複合体: human SAGA
      • タンパク質・ペプチド: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein
      • タンパク質・ペプチド: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
      • タンパク質・ペプチド: Isoform 3 of Transcription factor SPT20 homolog
      • タンパク質・ペプチド: Transcription initiation factor TFIID subunit 9B
      • タンパク質・ペプチド: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
      • タンパク質・ペプチド: Transcription initiation factor TFIID subunit 12
      • タンパク質・ペプチド: Transcription initiation factor TFIID subunit 10
      • タンパク質・ペプチド: Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog
      • タンパク質・ペプチド: Transcriptional adapter 1
      • タンパク質・ペプチド: Ataxin-7
    • 複合体: STAGA complex 65 subunit gamma
      • タンパク質・ペプチド: 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
  • リガンド: INOSITOL HEXAKISPHOSPHATE

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超分子 #1: human SAGA

超分子名称: human SAGA / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#11 / 詳細: endogeneous human SAGA purified from HeLa cells
分子量理論値: 1.420272 MDa

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超分子 #2: human SAGA

超分子名称: human SAGA / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1-#3, #5-#11 / 詳細: endogeneous human SAGA purified from HeLa cells
由来(天然)生物種: Homo sapiens (ヒト) / 株: HeLa / 組織: cervix

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超分子 #3: STAGA complex 65 subunit gamma

超分子名称: STAGA complex 65 subunit gamma / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #4
由来(天然)生物種: Homo sapiens (ヒト)

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分子 #1: Transformation/transcription domain-associated protein,Transforma...

分子名称: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated ...名称: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein
タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 353.170281 KDa
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)ET LRPLAYSTLA DLVHHVRQHL PLSDLSLAVQ LFAKNIDDES LPSSIQTMSC KLLLNLVDCI RSKSEQESGN GRD VLMRML EVFVLKFHTI ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)ET LRPLAYSTLA DLVHHVRQHL PLSDLSLAVQ LFAKNIDDES LPSSIQTMSC KLLLNLVDCI RSKSEQESGN GRD VLMRML EVFVLKFHTI ARYQLSAIFK KCKPQSELGA VEAALPGVPT APAAPGPAPS PAPVPAPPPP PPPPPPATPV TPAP VPPFE KQGEKDKEDK QTFQVTDCRS LVKTLVCGVK TITWGITSCK APGAQFIPNK QLQPKETQIY IKLVKYAMQA LDIYQ VQIA GNGQTYIRVA NCQTVRMKEE KEVLEHFAGV FTMMNPLTFK EIFQTTVPYM VERISKNYAL QIVANSFLAN PTTSAL FAT ILVEYLLDRL PEMGSNVELS NLYLKLFKLV FGSVSLFAAE NEQMLKPHLH KIVNSSMELA QTAKEPYNYF LLLRALF RS IGGGSHDLLY QEFLPLLPNL LQGLNMLQSG LHKQHMKDLF VELCLTVPVR LSSLLPYLPM LMDPLVSALN GSQTLVSQ G LRTLELCVDN LQPDFLYDHI QPVRAELMQA LWRTLRNPAD SISHVAYRVL GKFGGSNRKM LKESQKLHYV VTEVQGPSI TVEFSDCKAS LQLPMEKAIE TALDCLKSAN TEPYYRRQAW EVIKCFLVAM MSLEDNKHAL YQLLAHPNFT EKTIPNVIIS HRYKAQDTP ARKTFEQALT GAFMSAVIKD LRPSALPFVA SLIRHYTMVA VAQQCGPFLL PCYQVGSQPS TAMFHSEENG S KGMDPLVL IDAIAICMAY EEKELCKIGE VALAVIFDVA SIILGSKERA CQLPLFSYIV ERLCACCYEQ AWYAKLGGVV SI KFLMERL PLTWVLQNQQ TFLKALLFVM MDLTGEVSNG AVAMAKTTLE QLLMRCATPL KDEERAEEIV AAQEKSFHHV THD LVREVT SPNSTVRKQA MHSLQVLAQV TGKSVTVIME PHKEVLQDMV PPKKHLLRHQ PANAQIGLME GNTFCTTLQP RLFT MDLNV VEHKVFYTEL LNLCEAEDSA LTKLPCYKSL PSLVPLRIAA LNALAACNYL PQSREKIIAA LFKALNSTNS ELQEA GEAC MRKFLEGATI EVDQIHTHMR PLLMMLGDYR SLTLNVVNRL TSVTRLFPNS FNDKFCDQMM QHLRKWMEVV VITHKG GQR SDGNEMKICS AIINLFHLIP AAPQTLVKPL LEVVMKTERA MLIEAGSPFR EPLIKFLTRH PSQTVELFMM EATLNDP QW SRMFMSFLKH KDARPLRDVL AANPNRFITL LLPGGAQTAV RPGSPSTSTM RLDLQFQAIK IISIIVKNDD SWLASQHS L VSQLRRVWVS ENFQERHRKE NMAATNWKEP KLLAYCLLNY CKRN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)AGTSELVM LS LELVKTR LAVMSMEMRK NFIQAILTSL IEKSPDAKIL RAVVKIVEEW VKNNSPMAAN QTPTLREKSI LLVKMMTYIE KRF PEDLEL NAQFLDLVNY VYRDETLSGS ELTAKLEPAF LSGLRCAQPL IRAKFFEVFD NSMKRRVYER LLYVTCSQNW EAMG NHFWI KQCIELLLAV CEKSTPIGTS CQGAMLPSIT NVINLADSHD RAAFAMVTHV KQEPRERENS ESKEEDVEID IELAP GDQT STPKTKELSE KDIGNQLHML TNRHDKFLDT LREVKTGALL SAFVQLCHIS TTLAEKTWVQ LFPRLWKILS DRQQHA LAG EISPFLCSGS HQVQRDCQPS ALNCFVEAMS QCVPPIPIRP CVLKYLGKTH NLWFRSTLML EHQAFEKGLS LQIKPKQ TT EFYEQESITP PQQEILDSLA ELYSLLQEED MWAGLWQKRC KYSETATAIA YEQHGFFEQA QESYEKAMDK AKKEHERS N ASPAIFPEYQ LWEDHWIRCS KELNQWEALT EYGQSKGHIN PYLVLECAWR VSNWTAMKEA LVQVEVSCPK EMAWKVNMY RGYLAICHPE EQQLSFIERL VEMASSLAIR EWRRLPHVVS HVHTPLLQAA QQIIELQEAA QINAGLQPTN LGRNNSLHDM KTVVKTWRN RLPIVSDDLS HWSSIFMWRQ HHYQAIVTAY ENSSQHDPSS NNAMLGVHAS ASAIIQYGKI ARKQGLVNVA L DILSRIHT IPTVPIVDCF QKIRQQVKCY LQLAGVMGKN ECMQGLEVIE STNLKYFTKE MTAEFYALKG MFLAQINKSE EA NKAFSAA VQMHDVLVKA WAMWGDYLEN IFVKERQLHL GVSAITCYLH ACRHQNESKS RKYLAKVLWL LSFDDDKNTL ADA VDKYCI GVPPIQWLAW IPQLLTCLVG SEGKLLLNLI SQVGRVYPQA VYFPIRTLYL TLKIEQRERY KSDSGQQQPS SVGN QSHSA SDPGPIRATA PMWRCSRIMH MQRELHPTLL SSLEGIVDQM VWFRENWHEE VLRQLQQGLA KCYSVAFEKS GAVSD AKIT PHTLNFVKKL VSTFGVGLEN VSNVSTMFSS AASESLARRA QATAQDPVFQ KLKGQFTTDF DFSVPGSMKL HNLISK LKK WIKILEAKTK QLPKFFLIEE KCRFLSNFSA QTAEVEIPGE FLMPKPTHYY IKIARFMPRV EIVQKHNTAA RRLYIRG HN GKIYPYLVMN DACLTESRRE ERVLQLLRLL NPCLEKRKET TKRHLFFTVP RVVAVSPQMR LVEDNPSSLS LVEIYKQR C AKKGIEHDNP ISRYYDRLAT VQARGTQASH QVLRDILKEV QSNMVPRSML KEWALHTFPN ATDYWTFRKM FTIQLALIG FAEFVLHLNR LNPEMLQIAQ DTGKLNVAYF RFDINDATGD LDANRPVPFR LTPNISEFLT TIGVSGPLTA SMIAVARCFA QPNFKVDGI LKTVLRDEII AWHKKTQEDT SSPLSAAGQP ENMDSQQLVS LVQKAVTAIM TRLHNLAQFE GGESKVNTLV A AANSLDNL CRMDPAWHPW L

UniProtKB: Transformation/transcription domain associated protein, Transformation/transcription domain associated protein

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分子 #2: TAF5-like RNA polymerase II p300/CBP-associated factor-associated...

分子名称: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 66.223047 KDa
配列文字列: MKRVRTEQIQ MAVSCYLKRR QYVDSDGPLK QGLRLSQTAE EMAANLTVQS ESGCANIVSA APCQAEPQQY EVQFGRLRNF LTDSDSQHS HEVMPLLYPL FVYLHLNLVQ NSPKSTVESF YSRFHGMFLQ NASQKDVIEQ LQTTQTIQDI LSNFKLRAFL D NKYVVRLQ ...文字列:
MKRVRTEQIQ MAVSCYLKRR QYVDSDGPLK QGLRLSQTAE EMAANLTVQS ESGCANIVSA APCQAEPQQY EVQFGRLRNF LTDSDSQHS HEVMPLLYPL FVYLHLNLVQ NSPKSTVESF YSRFHGMFLQ NASQKDVIEQ LQTTQTIQDI LSNFKLRAFL D NKYVVRLQ EDSYNYLIRY LQSDNNTALC KVLTLHIHLD VQPAKRTDYQ LYASGSSSRS ENNGLEPPDM PSPILQNEAA LE VLQESIK RVKDGPPSLT TICFYAFYNT EQLLNTAEIS PDSKLLAAGF DNSCIKLWSL RSKKLKSEPH QVDVSRIHLA CDI LEEEDD EDDNAGTEMK ILRGHCGPVY STRFLADSSG LLSCSEDMSI RYWDLGSFTN TVLYQGHAYP VWDLDISPYS LYFA SGSHD RTARLWSFDR TYPLRIYAGH LADVDCVKFH PNSNYLATGS TDKTVRLWSA QQGNSVRLFT GHRGPVLSLA FSPNG KYLA SAGEDQRLKL WDLASGTLYK ELRGHTDNIT SLTFSPDSGL IASASMDNSV RVWDIRNTYC SAPADGSSSE LVGVYT GQM SNVLSVQFMA CNLLLVTGIT QENQEH

UniProtKB: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L

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分子 #3: Isoform 3 of Transcription factor SPT20 homolog

分子名称: Isoform 3 of Transcription factor SPT20 homolog / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 88.12907 KDa
配列文字列: MQQALELALD RAEYVIESAR QRPPKRKYLS SGRKSVFQKL YDLYIEECEK EPEVKKLRRN VNLLEKLVMQ ETLSCLVVNL YPGNEGYSL MLRGKNGSDS ETIRLPYEEG ELLEYLDAEE LPPILVDLLE KSQVNIFHCG CVIAEIRDYR QSSNMKSPGY Q SRHILLRP ...文字列:
MQQALELALD RAEYVIESAR QRPPKRKYLS SGRKSVFQKL YDLYIEECEK EPEVKKLRRN VNLLEKLVMQ ETLSCLVVNL YPGNEGYSL MLRGKNGSDS ETIRLPYEEG ELLEYLDAEE LPPILVDLLE KSQVNIFHCG CVIAEIRDYR QSSNMKSPGY Q SRHILLRP TMQTLICDVH SITSDNHKWT QEDKLLLESQ LILATAEPLC LDPSIAVTCT ANRLLYNKQK MNTRPMKRCF KR YSRSSLN RQQDLSHCPP PPQLRLLDFL QKRKERKAGQ HYDLKISKAG NCVDMWKRSP CNLAIPSEVD VEKYAKVEKS IKS DDSQPT VWPAHDVKDD YVFECEAGTQ YQKTKLTILQ SLGDPLYYGK IQPCKADEES DSQMSPSHSS TDDHSNWFII GSKT DAERV VNQYQELVQN EAKCPVKMSH SSSGSASLSQ VSPGKETDQT ETVSVQSSVL GKGVKHRPPP IKLPSSSGNS SSGNY FTPQ QTSSFLKSPT PPPSSKPSSI PRKSSVDLNQ VSMLSPAALS PASSSQRSGT PKPSTPTPTP SSTPHPPDAQ SSTPST PSA TPTPQDSGFT PQPTLLTQFA QQQRSLSQAM PVTTIPLSTM VTSITPGTTA TQVMANSAGL NFINVVGSVC GAQALMS GS NPMLGCNTGA ITPAGINLSG LLPSGGLLPN ALPSAMQAAS QAGVPFGLKN TSSLRPLNLL QLPGGSLIFN TLQQQQQQ L SQFTPQQPQQ PTTCSPQQPG EQGSEQGSTS QEQALSAQQA AVINLTGVGS FMQSQAAAVA ILAASNGYGS SSSTNSSAT SSSAYRQPVK K

UniProtKB: Transcription factor SPT20 homolog

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分子 #4: STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamm...

分子名称: 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
タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: unclassified Rhodococcus (バクテリア)
分子量理論値: 78.079922 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MLDIP SEPCSLTIH TIQLIQHNRR LRNLIATAQA QN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MLDIP SEPCSLTIH TIQLIQHNRR LRNLIATAQA QN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)DCKNP NAPFQIRHSD PESDFYRGK GEPVTELSWH SCRQLLYQAV ATILAHAGFD CANESVLETL TDVAHEYCLK FTKLLRFAVD REARLGQTPF P DVMEQVFH EVGIGSVLSL QKFWQHRIKD YHSYMLQISK QLSEEYERIV NPEKATEDAK PVKIKEEPVS DITFPVSEEL EA DLASGDQ SLPMGVLGAQ SERFPSNLEV EASPQASSAE VNASPLWNLA HVKMEPQESE EGNVSGHGVL GSDVFEEPMS GMS EAGIPQ SPDDSDSSYG SHSTDSLMGS SPVFNQRCKK RMRKIGTSGE DLYFQSGGSM AEIGTGFPFD PHYVEVLGER MHYV DVGPR DGTPVLFLHG NPTSSYVWRN IIPHVAPTHR CIAPDLIGMG KSDKPDLGYF FDDHVRFMDA FIEALGLEEV VLVIH DWGS ALGFHWAKRN PERVKGIAFM EFIRPIPTWD EWPEFARETF QAFRTTDVGR KLIIDQNVFI EGTLPMGVVR PLTEVE MDH YREPFLNPVD REPLWRFPNE LPIAGEPANI VALVEEYMDW LHQSPVPKLL FWGTPGVLIP PAEAARLAKS LPNCKAV DI GPGLNLLQED NPDLIGSEIA RWLSTLEISG DYKDHDGDYK DHDIDYKDDD DKGS

UniProtKB: STAGA complex 65 subunit gamma, STAGA complex 65 subunit gamma

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分子 #5: Transcription initiation factor TFIID subunit 9B

分子名称: Transcription initiation factor TFIID subunit 9B / タイプ: protein_or_peptide / ID: 5 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 27.654861 KDa
配列文字列: MESGKMAPPK NAPRDALVMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKPNVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQK NQTPLPLIKP YAGPRLPPDR YCLTAPNYRL KSLIKKGPNQ GRLVPRLSVG AVSSKPTTPT I ATPQTVSV ...文字列:
MESGKMAPPK NAPRDALVMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKPNVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQK NQTPLPLIKP YAGPRLPPDR YCLTAPNYRL KSLIKKGPNQ GRLVPRLSVG AVSSKPTTPT I ATPQTVSV PNKVATPMSV TSQRFTVQIP PSQSTPVKPV PATTAVQNVL INPSMIGPKN ILITTNMVSS QNTANEANPL KR KHEDDDD NDIM

UniProtKB: Transcription initiation factor TFIID subunit 9B

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分子 #6: TAF6-like RNA polymerase II p300/CBP-associated factor-associated...

分子名称: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
タイプ: protein_or_peptide / ID: 6 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 67.903289 KDa
配列文字列: MSEREERRFV EIPRESVRLM AESTGLELSD EVAALLAEDV CYRLREATQN SSQFMKHTKR RKLTVEDFNR ALRWSSVEAV CGYGSQEAL PMRPAREGEL YFPEDREVNL VELALATNIP KGCAETAVRV HVSYLDGKGN LAPQGSVPSA VSSLTDDLLK Y YHQVTRAV ...文字列:
MSEREERRFV EIPRESVRLM AESTGLELSD EVAALLAEDV CYRLREATQN SSQFMKHTKR RKLTVEDFNR ALRWSSVEAV CGYGSQEAL PMRPAREGEL YFPEDREVNL VELALATNIP KGCAETAVRV HVSYLDGKGN LAPQGSVPSA VSSLTDDLLK Y YHQVTRAV LGDDPQLMKV ALQDLQTNSK IGALLPYFVY VVSGVKSVSH DLEQLHRLLQ VARSLFRNPH LCLGPYVRCL VG SVLYCVL EPLAASINPL NDHWTLRDGA ALLLSHIFWT HGDLVSGLYQ HILLSLQKIL ADPVRPLCCH YGAVVGLHAL GWK AVERVL YPHLSTYWTN LQAVLDDYSV SNAQVKADGH KVYGAILVAV ERLLKMKAQA AEPNRGGPGG RGCRRLDDLP WDSL LFQES SSGGGAEPSF GSGLPLPPGG AGPEDPSLSV TLADIYRELY AFFGDSLATR FGTGQPAPTA PRPPGDKKEP AAAPD SVRK MPQLTASAIV SPHGDESPRG SGGGGPASAS GPAASESRPL PRVHRARGAP RQQGPGTGTR DVFQKSRFAP RGAPHF RFI IAGRQAGRRC RGRLFQTAFP APYGPSPASR YVQKLPMIGR TSRPARRWAL SDYSLYLPL

UniProtKB: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L

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分子 #7: Transcription initiation factor TFIID subunit 12

分子名称: Transcription initiation factor TFIID subunit 12 / タイプ: protein_or_peptide / ID: 7 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 17.948467 KDa
配列文字列:
MNQFGPSALI NLSNFSSIKP EPASTPPQGS MANSTAVVKI PGTPGAGGRL SPENNQVLTK KKLQDLVREV DPNEQLDEDV EEMLLQIAD DFIESVVTAA CQLARHRKSS TLEVKDVQLH LERQWNMWIP GFGSEEIRPY KKACTTEAHK QRMALIRKTT K K

UniProtKB: Transcription initiation factor TFIID subunit 12

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分子 #8: Transcription initiation factor TFIID subunit 10

分子名称: Transcription initiation factor TFIID subunit 10 / タイプ: protein_or_peptide / ID: 8 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 21.731248 KDa
配列文字列: MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN ...文字列:
MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN DALQHCKMKG TASGSSRSKS KDRKYTLTME DLTPALSEYG INVKKPHYFT

UniProtKB: Transcription initiation factor TFIID subunit 10

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分子 #9: Transcription initiation protein SPT3 homolog,Transcription initi...

分子名称: Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog
タイプ: protein_or_peptide / ID: 9 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 33.197047 KDa
配列文字列: MNNTAASPMS TATSSSGRST GKSISFATEL QSMMYSLGDA RRPLHETAVL VEDVVHTQLI NLLQQAAEVS QLRGARVITP EDLLFLMRK DKKKLRRLLK YMFIRDYKSK IVKGIDEDDL LEDKLSGSNN ANKRQKIAQD FLNSIDQTGE LLAMFED (UNK)(UNK) (UNK) ...文字列:
MNNTAASPMS TATSSSGRST GKSISFATEL QSMMYSLGDA RRPLHETAVL VEDVVHTQLI NLLQQAAEVS QLRGARVITP EDLLFLMRK DKKKLRRLLK YMFIRDYKSK IVKGIDEDDL LEDKLSGSNN ANKRQKIAQD FLNSIDQTGE LLAMFED (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ESRQLSFSKK ASKFRDWLDC SSMEIKPNV VAMEILAYLA YETVAQLVDL ALLVRQDMVT KAGDPFSHAI SATFIQYHNS AESTAACGVE AHSDAIQPCH I REAIRRYS HRIGPLSPFT NAYRRNGMAF LAC

UniProtKB: Transcription initiation protein SPT3 homolog, Transcription initiation protein SPT3 homolog

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分子 #10: Transcriptional adapter 1

分子名称: Transcriptional adapter 1 / タイプ: protein_or_peptide / ID: 10 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 37.432531 KDa
配列文字列: MATFVSELEA AKKNLSEALG DNVKQYWANL KLWFKQKISK EEFDLEAHRL LTQDNVHSHN DFLLAILTRC QILVSTPDGA GSLPWPGGS AAKPGKPKGK KKLSSVRQKF DHRFQPQNPL SGAQQFVAKD PQDDDDLKLC SHTMMLPTRG QLEGRMIVTA Y EHGLDNVT ...文字列:
MATFVSELEA AKKNLSEALG DNVKQYWANL KLWFKQKISK EEFDLEAHRL LTQDNVHSHN DFLLAILTRC QILVSTPDGA GSLPWPGGS AAKPGKPKGK KKLSSVRQKF DHRFQPQNPL SGAQQFVAKD PQDDDDLKLC SHTMMLPTRG QLEGRMIVTA Y EHGLDNVT EEAVSAVVYA VENHLKDILT SVVSRRKAYR LRDGHFKYAF GSNVTPQPYL KNSVVAYNNL IESPPAFTAP CA GQNPASH PPPDDAEQQA ALLLACSGDT LPASLPPVNM YDLFEALQVH REVIPTHTVY ALNIERIITK LWHPNHEELQ QDK VHRQRL AAKEGLLLC

UniProtKB: Transcriptional adapter 1

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分子 #11: Ataxin-7

分子名称: Ataxin-7 / タイプ: protein_or_peptide / ID: 11 / コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 95.597742 KDa
配列文字列: MSERAADDVR GEPRRAAAAA GGAAAAAARQ QQQQQQQQQP PPPQPQRQQH PPPPPRRTRP EDGGPGAAST SAAAMATVGE RRPLPSPEV MLGQSWNLWV EASKLPGKDG TELDESFKEF GKNREVMGLC REDMPIFGFC PAHDDFYLVV CNDCNQVVKP Q AFQSHYER ...文字列:
MSERAADDVR GEPRRAAAAA GGAAAAAARQ QQQQQQQQQP PPPQPQRQQH PPPPPRRTRP EDGGPGAAST SAAAMATVGE RRPLPSPEV MLGQSWNLWV EASKLPGKDG TELDESFKEF GKNREVMGLC REDMPIFGFC PAHDDFYLVV CNDCNQVVKP Q AFQSHYER RHSSSSKPPL AVPPTSVFSF FPSLSKSKGG SASGSNRSSS GGVLSASSSS SKLLKSPKEK LQLRGNTRPM HP IQQSRVP HGRIMTPSVK VEKIHPKMDG TLLKSAVGPT CPATVSSLVK PGLNCPSIPK PTLPSPGQIL NGKGLPAPPT LEK KPEDNS NNRKFLNKRL SEREFDPDIH CGVIDLDTKK PCTRSLTCKT HSLTQRRAVQ GRRKRFDVLL AEHKNKTREK ELIR HPDSQ QPPQPLRDPH PAPPRTSQEP HQNPHGVIPS ESKPFVASKP KPHTPSLPRP PGCPAQQGGS APIDPPPVHE SPHPP LPAT EPASRLSSEE GEGDDKEESV EKLDCHYSGH HPQPASFCTF GSRQIGRGYY VFDSRWNRLR CALNLMVEKH LNAQLW KKI PPVPSTTSPI STRIPHRTNS VPTSQCGVSY LAAATVSTSP VLLSSTCISP NSKSVPAHGT TLNAQPAASG AMDPVCS MQ SRQVSSSSSS PSTPSGLSSV PSSPMSRKPQ KLKSSKSLRP KESSGNSTNC QNASSSTSGG SGKKRKNSSP LLVHSSSS S SSSSSSSHSM ESFRKNCVAH SGPPYPSTVT SSHSIGLNCV TNKANAVNVR HDQSGRGPPT GSPAESIKRM SVMVNSSDS TLSLGPFIHQ SNELPVNSHG SFSHSHTPLD KLIGKKRKCS PSSSSINNSS SKPTKVAKVP AVNNVHMKHT GTIPGAQGLM NSSLLHQPK ARP

UniProtKB: Ataxin-7

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分子 #12: INOSITOL HEXAKISPHOSPHATE

分子名称: INOSITOL HEXAKISPHOSPHATE / タイプ: ligand / ID: 12 / コピー数: 1 / 式: IHP
分子量理論値: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / フィチン酸

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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

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試料調製

緩衝液pH: 7.8
構成要素:
濃度名称式
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMsodium chlorideNaCl
0.2 mMEthylenediaminetetraacetic acid
0.5 mMtris(2-carboxyethyl)phosphine
0.01 % (v/v)nonyl phenoxypolyethoxylethanol
2.5 % (v/v)Glycerol

詳細: Buffers were freshly prepared and 0.22 um filtered.
グリッドモデル: UltrAuFoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: GRAPHENE OXIDE / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 59 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 101.325 kPa
凍結凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV / 詳細: blot force 0, blot time 3 sec.
詳細The sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
特殊光学系エネルギーフィルター - 名称: GIF Bioquantum
撮影フィルム・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 / 平均電子線量: 50.0 e/Å2
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 50.0 µm / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス（公称値）: 3.4 µm / 最小 デフォーカス（公称値）: 0.9 µm / 倍率（公称値）: 64000
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
ホルダー冷却材: NITROGEN
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

粒子像選択選択した数: 2438694
初期モデルモデルのタイプ: OTHER
詳細: negative stain reconstruction, see related entry EMD-23028 (7KTS)
最終 再構成使用したクラス数: 2 / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 2.93 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.1) / 使用した粒子像数: 209435
初期 角度割当タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 3.1)
最終 角度割当タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 3.1)
最終 3次元分類クラス数: 5 / 平均メンバー数/クラス: 71488 / ソフトウェア - 名称: RELION (ver. 3.1)
FSC曲線 (解像度の算出)

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原子モデル構築 1

精密化空間: REAL / プロトコル: AB INITIO MODEL
得られたモデル

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

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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

他の情報も見る