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- EMDB-10120: Structure of nucleotide-bound Tel1/ATM -

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基本情報

登録情報
データベース: EMDB / ID: EMD-10120
タイトルStructure of nucleotide-bound Tel1/ATM
マップデータTel1 Whole Dimer
試料
  • 複合体: Tel1/ATM
    • タンパク質・ペプチド: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1
  • リガンド: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • リガンド: MAGNESIUM ION
キーワードKinase (キナーゼ) / DNA Damage Response / CryoEM (低温電子顕微鏡法) / Phosphatidylinositol-3-kinase-like kinase / HYDROLASE (加水分解酵素)
機能・相同性
機能・相同性情報


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / telomeric DNA binding / signal transduction in response to DNA damage / negative regulation of TORC1 signaling / telomere maintenance / DNA damage checkpoint signaling / double-strand break repair ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / telomeric DNA binding / signal transduction in response to DNA damage / negative regulation of TORC1 signaling / telomere maintenance / DNA damage checkpoint signaling / double-strand break repair / chromatin organization / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / リン酸化 / protein serine kinase activity / DNA修復 / protein serine/threonine kinase activity / DNA damage response / ミトコンドリア / ATP binding / 細胞核
類似検索 - 分子機能
Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. ...Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Serine/threonine-protein kinase TEL1
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å
データ登録者Yates LA / Williams RM
資金援助 英国, 1件
OrganizationGrant number国
Wellcome Trust 英国
引用ジャーナル: Structure / 年: 2020
タイトル: Cryo-EM Structure of Nucleotide-Bound Tel1 Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations.
著者: Luke A Yates / Rhys M Williams / Sarem Hailemariam / Rafael Ayala / Peter Burgers / Xiaodong Zhang /
要旨: Yeast Tel1 and its highly conserved human ortholog ataxia-telangiectasia mutated (ATM) are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia- ...Yeast Tel1 and its highly conserved human ortholog ataxia-telangiectasia mutated (ATM) are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia (A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Using cryoelectron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Our structure reveals molecular details of key residues surrounding the nucleotide binding site and provides a structural and molecular basis for its intrinsically low basal activity. We show that the catalytic residues are in a productive conformation for catalysis, but the phosphatidylinositol 3-kinase-related kinase (PIKK) regulatory domain insert restricts peptide substrate access and the N-lobe is in an open conformation, thus explaining the requirement for Tel1 activation. Structural comparisons with other PIKKs suggest a conserved and common allosteric activation mechanism. Our work also provides a structural rationale for many mutations found in A-T and cancer.
履歴
登録2019年7月9日-
ヘッダ(付随情報) 公開2019年10月30日-
マップ公開2019年10月30日-
更新2024年5月22日-
現状2024年5月22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: 0.02
  • 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: 0.02
  • 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-6s8f
  • 表面レベル: 0.02
  • 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_10120.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_10120.map.gz / 形式: CCP4 / 大きさ: 209.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Tel1 Whole Dimer
ボクセルのサイズX=Y=Z: 1.085 Å
密度
表面レベル登録者による: 0.02 / ムービー #1: 0.02
最小 - 最大-0.032512594 - 0.08536378
平均 (標準偏差)-0.00027760275 (±0.00329771)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ380380380
Spacing380380380
セルA=B=C: 412.30002 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z412.300412.300412.300
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ307236
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0330.085-0.000

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添付データ

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追加マップ: Tel1 Kinase Core Dimer

ファイルemd_10120_additional_1.map
注釈Tel1 Kinase Core Dimer
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: Tel1 FATKIN Dimer

ファイルemd_10120_additional_2.map
注釈Tel1 FATKIN Dimer
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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試料の構成要素

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全体 : Tel1/ATM

全体名称: Tel1/ATM
要素
  • 複合体: Tel1/ATM
    • タンパク質・ペプチド: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1
  • リガンド: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • リガンド: MAGNESIUM ION

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超分子 #1: Tel1/ATM

超分子名称: Tel1/ATM / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)

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分子 #1: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kin...

分子名称: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1
タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: non-specific serine/threonine protein kinase
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 292.579406 KDa
組換発現生物種: Saccharomyces cerevisiae (パン酵母)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
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(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)GS IRGGKQRVFA TFIKCLQKLD SSNIINIMNS ISSYMAQV S YKNQSIIFYE IKSLFGPPQQ SIEKSAFYSL AMSMLSLVSY PSLVFSLEDM MTYSGFNHTR AFIQQALNKI TVAFRYQNL TELFEYCKFD LIMYWFNRTK VPTSKLEKEW DISLFGFADI HEFLGRYFVE ISAIYFSQGF NQKWILDMLH AITGNGDAYL VDNSYYLCI PLAFISGGVN ELIFDILPQI SGKTTVKYHK KYRLLMLKWI IRFTDLGSLT ELRSTVEKLF PTSYLSPYLF E NSSVSMRY QYPLHIPLAL GATLVQTQFA HEKNNTHEFK LLFLSVITDL EKTSTYIGKL RCARELKYLF VLYENVLVKS ST LNFIIIR LSKFLIDTQI HDEVITIFSS LLNLADKNTF EIEPSLPNLF CKIFIYLREN KQLSPSFQQA IKLLEHRDLI KIK TWKYCL DAIFGNIVQD DIYENTELLD ASDCGVDDVV LVSLLFSYAR RPVASKIGCS LSKAAAINIL KHHVPKEYLS KNFK LWFAA LSRRILQQEV QRERSTNFNN EVHLKNFEMV FRHPEQPHMI YQRISTFNKE AELYDSTEVF FISECILTYL VGYSI GNSE SEFCFRDNIM NENKDKVAPL DKDVLNAIYP LANNFGMESF ICDTYLSVNE PYNCWLSKFA RSLIHQISFN IPPIVC LYP LCKGSTAFCE LVLTDLFFLS TTYDPKSCLN WSNRIFTQIA MLLHVKDSEI KLKMLFNVIK MIRMGSRCKE RNCLRIY SS LDLQEICQIS LKIKEFKFGY LLFEEMNMPN IREMNINTLQ KIYECINDGD FLAGLPVPHS IEGVLNSINR IDSDTWKR F LFNNADFDAN YTTSLEEEKE SLIKATEDSG FYGLTSLLES RLSGSSDVYK WNLELGDWKL LTPKVVDSKA KGLYYAIKN LPQDVGFAEK SLEKSLLTIF DSRQHFISQT EWMDTLNAII EFIKIAAIPQ DVTSFPQTLM SIMKADKERL NTIDFYDHKT TLKSRHTLM NVLSRNSLDE NVKCSKYLRL GSIIQLANYV QLAIANGAPQ DALRNATLMS KTVKNIAKLY DDPSVVSQIE K LASFTSAN ALWESREYKA PVMIMRDLLA QNEKNISESI LYDDFKLLIN VPMDQIKARL VKWSSESRLE PAAAIYEKII VN WDINVED HESCSDVFYT LGSFLDEQAQ KLRSNGEIED REHRSYTGKS TLKALELIYK NTKLPENERK DAKRHYNRVL LQY NRDSEV LKALLLQKEK FLWHALHFYL NTLVFSNRYD NDIIDKFCGL WFENDDNSKI NQLLYKEIGT IPSWKFLPWV NQIA SKISM EENEFQKPLQ LTMKRLLYKL PYDSLYSVMS ILLYEKQSNK DTNISQKIQA VKKILLELQG YDRGAFAKKY LLPVQ EFCE MSVELANLKF VQNTKTLRLA NLKIGQYWLK QLNMEKLPLP TSNFTVKSSA DGRKARPYIV SVNETVGITT TGLSLP KIV TFNISDGTTQ KALMKGSNDD LRQDAIMEQV FQQVNKVLQN DKVLRNLDLG IRTYKVVPLG PKAGIIEFVA NSTSLHQ IL SKLHTNDKIT FDQARKGMKA VQTKSNEERL KAYLKITNEI KPQLRNFFFD SFPDPLDWFE AKKTYTKGVA ASSIVGYI L GLGDRHLNNI LLDCSTGEPI HIDLGIAFDQ GKLLPIPELV PFRLTRDIVD GFGVTGVDGL FRRSCERVYA VLRKDYVKV MCVLNILKWD PLYSWVMSPV KKYEHLFEEE HEITNFDNVS KFISNNDRNE NQESYRALKG VEEKLMGNGL SVESSVQDLI QQATDPSNL SVIYMGWSPF Y

UniProtKB: Serine/threonine-protein kinase TEL1

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分子 #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

分子名称: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / タイプ: ligand / ID: 2 / コピー数: 2 / 式: ANP
分子量理論値: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP / AMP-PNP, エネルギー貯蔵分子類似体*YM

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分子 #3: MAGNESIUM ION

分子名称: MAGNESIUM ION / タイプ: ligand / ID: 3 / コピー数: 2 / 式: MG
分子量理論値: 24.305 Da

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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: 7.4
凍結凍結剤: ETHANE

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy
撮影フィルム・検出器のモデル: FEI FALCON III (4k x 4k)
平均電子線量: 88.8 e/Å2
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

初期モデルモデルのタイプ: EMDB MAP
EMDB ID:

4097

初期 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0)
最終 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0)
最終 再構成想定した対称性 - 点群: C2 (2回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0) / 使用した粒子像数: 167596
FSC曲線 (解像度の算出)

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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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