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- EMDB-12979: Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex -

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基本情報

登録情報
データベース: EMDB / ID: EMD-12979
タイトルCryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex
マップデータStructure of the TELO2-TTI1-TTI2 complex and its function in TOR recruitment to the R2TP chaperone
試料
  • 複合体: TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex
    • タンパク質・ペプチド: RuvB-like 1
    • タンパク質・ペプチド: RuvB-like 2
    • タンパク質・ペプチド: TELO2-interacting protein 1 homolog,TELO2-interacting protein 1 homolog,TTI1
    • タンパク質・ペプチド: TELO2-interacting protein 2,TELO2-interacting protein 2,TTI2
    • タンパク質・ペプチド: Telomere length regulation protein TEL2 homolog
  • リガンド: ADENOSINE-5'-DIPHOSPHATE
機能・相同性
機能・相同性情報


: / positive regulation of DNA damage checkpoint / TTT Hsp90 cochaperone complex / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / TORC2 complex / TORC1 complex ...: / positive regulation of DNA damage checkpoint / TTT Hsp90 cochaperone complex / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / TORC2 complex / TORC1 complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / regulation of TOR signaling / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / protein folding chaperone complex / box C/D snoRNP assembly / regulation of chromosome organization / NuA4 histone acetyltransferase complex / telomeric DNA binding / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / telomere maintenance via telomerase / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / DNA helicase activity / positive regulation of DNA repair / TBP-class protein binding / telomere maintenance / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / Hsp90 protein binding / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / ADP binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / DNA helicase / chromosome, telomeric region / molecular adaptor activity / transcription coactivator activity / nuclear body / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / cadherin binding / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
Tti2 family / Tti2 family / TEL2-interacting protein 1 / : / TELO2-interacting protein 1 / Telomere length regulation protein, conserved domain / TEL2, C-terminal domain superfamily / Telomere length regulation protein / RuvB-like / RuvB-like, AAA-lid domain ...Tti2 family / Tti2 family / TEL2-interacting protein 1 / : / TELO2-interacting protein 1 / Telomere length regulation protein, conserved domain / TEL2, C-terminal domain superfamily / Telomere length regulation protein / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Armadillo-like helical / Armadillo-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
TELO2-interacting protein 1 homolog / TELO2-interacting protein 2 / RuvB-like 2 / RuvB-like 1 / Telomere length regulation protein TEL2 homolog
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.41 Å
データ登録者Pal M / Llorca O / Pearl L
資金援助 英国, スペイン, 5件
OrganizationGrant number国
Wellcome Trust095605/Z/11/Z 英国
Wellcome Trust095605/Z/11/A 英国
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R01678X/1 英国
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P スペイン
European Regional Development FundY2018/BIO4747 スペイン
引用ジャーナル: Cell Rep / 年: 2021
タイトル: Structure of the TELO2-TTI1-TTI2 complex and its function in TOR recruitment to the R2TP chaperone.
著者: Mohinder Pal / Hugo Muñoz-Hernandez / Dennis Bjorklund / Lihong Zhou / Gianluca Degliesposti / J Mark Skehel / Emma L Hesketh / Rebecca F Thompson / Laurence H Pearl / Oscar Llorca / Chrisostomos Prodromou /
要旨: The R2TP (RUVBL1-RUVBL2-RPAP3-PIH1D1) complex, in collaboration with heat shock protein 90 (HSP90), functions as a chaperone for the assembly and stability of protein complexes, including RNA ...The R2TP (RUVBL1-RUVBL2-RPAP3-PIH1D1) complex, in collaboration with heat shock protein 90 (HSP90), functions as a chaperone for the assembly and stability of protein complexes, including RNA polymerases, small nuclear ribonucleoprotein particles (snRNPs), and phosphatidylinositol 3-kinase (PI3K)-like kinases (PIKKs) such as TOR and SMG1. PIKK stabilization depends on an additional complex of TELO2, TTI1, and TTI2 (TTT), whose structure and function are poorly understood. The cryoelectron microscopy (cryo-EM) structure of the human R2TP-TTT complex, together with biochemical experiments, reveals the mechanism of TOR recruitment to the R2TP-TTT chaperone. The HEAT-repeat TTT complex binds the kinase domain of TOR, without blocking its activity, and delivers TOR to the R2TP chaperone. In addition, TTT regulates the R2TP chaperone by inhibiting RUVBL1-RUVBL2 ATPase activity and by modulating the conformation and interactions of the PIH1D1 and RPAP3 components of R2TP. Taken together, our results show how TTT couples the recruitment of TOR to R2TP with the regulation of this chaperone system.
履歴
登録2021年5月19日-
ヘッダ(付随情報) 公開2021年7月7日-
マップ公開2021年7月7日-
更新2021年10月6日-
現状2021年10月6日処理サイト: PDBe / 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: 0.0106
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（円筒半径に従い着色）
  • 表面レベル: 0.0106
  • 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-7ole
  • 表面レベル: 0.0106
  • UCSF Chimeraによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • 原子モデルPDB-7ole
  • Jmol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_12979.png

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マップ

ファイルダウンロード / ファイル: emd_12979.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Structure of the TELO2-TTI1-TTI2 complex and its function in TOR recruitment to the R2TP chaperone
ボクセルのサイズX=Y=Z: 1.07 Å
密度
表面レベル登録者による: 0.0106 / ムービー #1: 0.0106
最小 - 最大-0.018770417 - 0.053764913
平均 (標準偏差)0.00062394125 (±0.0026227725)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ280280280
Spacing280280280
セルA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0190.0540.001

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添付データ

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追加マップ: Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset1)...

ファイルemd_12979_additional_1.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset1)
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追加マップ: Cryo-EM structure of the TELO2-TTI1-TTI2 complex

ファイルemd_12979_additional_2.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2 complex
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追加マップ: Cryo-EM structure of the TELO2-TTI1-TTI2 complex

ファイルemd_12979_additional_3.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2 complex
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追加マップ: Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset1 halfmap1)...

ファイルemd_12979_additional_4.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset1 halfmap1)
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追加マップ: Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset1 halfmap2)...

ファイルemd_12979_additional_5.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset1 halfmap2)
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追加マップ: Composite map of the R2-TTT structure

ファイルemd_12979_additional_6.map
注釈Composite map of the R2-TTT structure
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ハーフマップ: Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset2)...

ファイルemd_12979_half_map_1.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset2)
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ハーフマップ: Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset2)...

ファイルemd_12979_half_map_2.map
注釈Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex (dataset2)
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試料の構成要素

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全体 : TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex

全体名称: TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex
要素
  • 複合体: TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex
    • タンパク質・ペプチド: RuvB-like 1
    • タンパク質・ペプチド: RuvB-like 2
    • タンパク質・ペプチド: TELO2-interacting protein 1 homolog,TELO2-interacting protein 1 homolog,TTI1
    • タンパク質・ペプチド: TELO2-interacting protein 2,TELO2-interacting protein 2,TTI2
    • タンパク質・ペプチド: Telomere length regulation protein TEL2 homolog
  • リガンド: ADENOSINE-5'-DIPHOSPHATE

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超分子 #1: TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex

超分子名称: TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#5
分子量実験値: 580 KDa

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分子 #1: RuvB-like 1

分子名称: RuvB-like 1 / タイプ: protein_or_peptide / ID: 1 / 詳細: ADP / コピー数: 3 / 光学異性体: LEVO / EC番号: DNA helicase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 50.296914 KDa
組換発現生物種: Escherichia coli BL21(DE3) (大腸菌)
配列文字列: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...文字列:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

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分子 #2: RuvB-like 2

分子名称: RuvB-like 2 / タイプ: protein_or_peptide / ID: 2 / 詳細: ADP / コピー数: 3 / 光学異性体: LEVO / EC番号: DNA helicase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 51.222465 KDa
組換発現生物種: Escherichia coli BL21(DE3) (大腸菌)
配列文字列: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...文字列:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

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分子 #3: TELO2-interacting protein 1 homolog,TELO2-interacting protein 1 h...

分子名称: TELO2-interacting protein 1 homolog,TELO2-interacting protein 1 homolog,TTI1
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: 176.844344 KDa
組換発現生物種: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾)
配列文字列: MAVFDTPEEA FGVLRPVCVQ LTKTQTVENV EHLQTRLQAV SDSALQELQQ YILFPLRFTL KTPGPKRERL IQSVVECLTF VLSSTCVKE QELLQELFSE LSACLYSPSS QKPAAVSEEL KLAVIQGLST LMHSAYGDII LTFYEPSILP RLGFAVSLLL G LAEQEKSK ...文字列:
MAVFDTPEEA FGVLRPVCVQ LTKTQTVENV EHLQTRLQAV SDSALQELQQ YILFPLRFTL KTPGPKRERL IQSVVECLTF VLSSTCVKE QELLQELFSE LSACLYSPSS QKPAAVSEEL KLAVIQGLST LMHSAYGDII LTFYEPSILP RLGFAVSLLL G LAEQEKSK QIKIAALKCL QVLLLQCDCQ DHPRSLDELE QKQLGDLFAS FLPGISTALT RLITGDFKQG HSIVVSSLKI FY KTVSFIM ADEQLKRISK VQAKPAVEHR VAELMVYREA DWVKKTGDKL TILIKKIIEC VSVHPHWKVR LELVELVEDL LLK CSQSLV ECAGPLLKAL VGLVNDESPE IQAQCNKVLR HFADQKVVVG NKALADILSE SLHSLATSLP RLMNSQDDQG KFST LSLLL GYLKLLGPKI NFVLNSVAHL QRLSKALIQV LELDVADIKI VEERRWNSDD LNASPKTSAT QPWNRIQRRY FRFFT DERI FMLLRQVCQL LGYYGNLYLL VDHFMELYHQ SVVYRKQAAM ILNELVTGAA GLEVEDLHEK HIKTNPEELR EIVTSI LEE YTSQENWYLV TCLETEEMGE ELMMEHPGLQ AITSGEHTCQ VTSFLAFSKP SPTICSMNSN IWQICIQLEG IGQFAYA LG KDFCLLLMSA LYPVLEKAGD QTLLISQVAT STMMDVCRAC GYDSLQHLIN QNSDYLVNGI SLNLRHLALH PHTPKVLE V MLRNSDANLL PLVADVVQDV LATLDQFYDK RAASFVSVLH ALMAALAQWF PDTGNLGHLQ EQSLGEEGSH LNQRPAALE KSTTTAEDIE QFLLNYLKEK DVADGNVSDF DNEEEEQSVP PKVDENDTRP DVEPPLPLQI QIAMDVMERC IHLLSDKNLQ IRLKVLDVL DLCVVVLQSH KNQLLPLAHQ AWPSLVHRLT RDAPLAVLRA FKVLRTLGSK CGDFLRSRFC KDVLPKLAGS L VTQAPISA RAGPVYSHTL AFKLQLAVLQ GLGPLCERLD LGEGDLNKVA DACLIYLSVK QPVKLQEAAR SVFLHLMKVD PD STWFLLN ELYCPVQFTP PHPSLHPVQL HGASGQQNPY TTNVLQLLKE LQ(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)G(UNK)G(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)G(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)G (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)G(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)G(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #4: TELO2-interacting protein 2,TELO2-interacting protein 2,TTI2

分子名称: TELO2-interacting protein 2,TELO2-interacting protein 2,TTI2
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: Homo sapiens (ヒト)
分子量理論値: 95.633781 KDa
組換発現生物種: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾)
配列文字列: MELDSALEAP SQEDSNLSEE LSHSAFGQAF SKILHCLARP EARRGNVKDA VLKDLGDLIE ATEFDRLFEG TGARLRGMPE TLGQVAKAL EKYAAPSKEE EGGGDGHSEA AEKAAQVGLL FLKLLGKVET AKNSLVGPAW QTGLHHLAGP VYIFAITHSL E QPWTTPRS ...文字列:
MELDSALEAP SQEDSNLSEE LSHSAFGQAF SKILHCLARP EARRGNVKDA VLKDLGDLIE ATEFDRLFEG TGARLRGMPE TLGQVAKAL EKYAAPSKEE EGGGDGHSEA AEKAAQVGLL FLKLLGKVET AKNSLVGPAW QTGLHHLAGP VYIFAITHSL E QPWTTPRS REVAREVLTS LLQVTECGSV AGFLHGENED EKGRLSVILG LLKPDLYKES WKNNPAIKHV FSWTLQQVTR PW LSQHLER VLPASLVISD DYQTENKILG VHCLHHIVLN VPAADLLQYN RAQVLYHAIS NHLYTPEHHL IQAVLLCLLD LFP ILEKTL HWKGDGARPT THCDEVLRLI LTHMEPEHRL LLRRTYARNL PAFVNRLGIL TVRHLKRLER VIIGYLEVYD GPEE EARLK ILETLKLLMQ HTWPRVSCRL VVLLKALLKL ICDVARDPNL TPESVKSALL QEATDCLILL DRCSQGRVKG LLAKI PQSC EDRKVVNYIR KVQQVSEGAP YNGT(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)G(UNK)G(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)G(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)G (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)G (UNK)(UNK)G (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #5: Telomere length regulation protein TEL2 homolog

分子名称: Telomere length regulation protein TEL2 homolog / タイプ: protein_or_peptide / ID: 5 / 詳細: LGEMEPPALPREKEEFASAHF / 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: 53.424195 KDa
組換発現生物種: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾)
配列文字列: MEPAPSEVRL AVREAIHALS SSEDGGHIFC TLESLKRYLG EMEPPALPRE (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)KEEFASAHF SPVLRCLASR LSPAWLELLP HGRLE(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) ...文字列:
MEPAPSEVRL AVREAIHALS SSEDGGHIFC TLESLKRYLG EMEPPALPRE (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)KEEFASAHF SPVLRCLASR LSPAWLELLP HGRLE(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)ELWASF FLEGPADQAF LVLMETIEGA AGPSFRLMKM ARLLARFLRE GRLAVLMEAQ CRQQTQPGF ILLRETLLGK VV(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)ALPDHLGNR LQQENLAEFF PQNYFRLLGE EVVRVLQAVV DSLQGGLDSS VSFVSQ VLG KACVHGRQQE ILGVLVPRLA ALTQGSYLHQ RVCWRLVEQV PDRAMEAVLT GLVEAALGPE VLSRLLGNLV VKNKKAQ FV MTQKLLFLQS RLTTPMLQSL LGHLAMDSQR RPLLLQVLKE LLETWGSSSA IRHTPLPQQR HVSKAVLICL AQLGEPEL R DSRDELLASM MAGVKCRLDS SLPPVRRLGM IVAEVVSARI HPEGPPLKFQ YEEDELSLEL LALASPQPAG DGASEAGT

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分子 #6: ADENOSINE-5'-DIPHOSPHATE

分子名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 6 / コピー数: 5 / 式: ADP
分子量理論値: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP / ADP, エネルギー貯蔵分子*YM

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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

濃度1 mg/mL
緩衝液pH: 7.5
構成要素:
濃度式名称
20.0 mMHEPES2-[4-(2-Hydroxyethyl)-1-piperazinyl]-ethanesulfonic acid
140.0 mMNaClSodium Chroride

詳細: Solutions were made fresh for protein purification
グリッドモデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR
凍結凍結剤: ETHANE-PROPANE / チャンバー内湿度: 90 % / チャンバー内温度: 287.15 K / 装置: LEICA PLUNGER / 詳細: 3sec.

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
温度最低: 90.0 K / 最高: 100.0 K
撮影フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
検出モード: COUNTING / デジタル化 - サイズ - 横: 1034 pixel / デジタル化 - サイズ - 縦: 1034 pixel / デジタル化 - サンプリング間隔: 5.0 µm / デジタル化 - 画像ごとのフレーム数: 1-40 / 撮影したグリッド数: 10 / 実像数: 6000 / 平均露光時間: 9.0 sec. / 平均電子線量: 60.17 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: 70.0 µm / 最大 デフォーカス（補正後）: 3.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最小 デフォーカス（公称値）: 1.2 µm / 倍率（公称値）: 130000
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: 1000
CTF補正ソフトウェア - 名称: RELION (ver. 3.1) / ソフトウェア - 詳細: CTFFIND
最終 再構成使用したクラス数: 200 / 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: BACK PROJECTION / 解像度のタイプ: BY AUTHOR / 解像度: 3.41 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) / ソフトウェア - 詳細: RELION / 使用した粒子像数: 267149
初期 角度割当タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 3.1) / ソフトウェア - 詳細: RELION
最終 角度割当タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 3.1) / ソフトウェア - 詳細: RELION
最終 3次元分類クラス数: 200 / 平均メンバー数/クラス: 100 / ソフトウェア - 名称: RELION (ver. 3.1) / ソフトウェア - 詳細: RELION
FSC曲線 (解像度の算出)

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原子モデル構築 1

初期モデルPDB ID:

6fo1

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

PDB-7ole:
Cryo-EM structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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