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- EMDB-13675: Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-ter... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-13675
タイトルHuman SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor
マップデータ
試料
  • 複合体: SMG1-SMG8-SMG9 kinase complex bound to a SMG1 inhibitor
    • タンパク質・ペプチド: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
    • タンパク質・ペプチド: Protein SMG8
    • タンパク質・ペプチド: Protein SMG9
  • リガンド: INOSITOL HEXAKISPHOSPHATEフィチン酸
  • リガンド: 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea
  • リガンド: ADENOSINE-5'-TRIPHOSPHATE
  • リガンド: MAGNESIUM ION
機能・相同性
機能・相同性情報


diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / eye development / regulation of telomere maintenance / regulation of protein kinase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus ...diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / eye development / regulation of telomere maintenance / regulation of protein kinase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / brain development / heart development / peptidyl-serine phosphorylation / in utero embryonic development / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / DNA修復 / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / RNA binding / 核質 / ATP binding / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / Serine/threonine-protein kinase SMG1 / Serine/threonine-protein kinase SMG1, N-terminal / SMG1, PIKK catalytic domain / Serine/threonine-protein kinase smg-1 / Serine/threonine-protein kinase SMG1 N-terminal / Rapamycin binding domain / FATC domain ...Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / Serine/threonine-protein kinase SMG1 / Serine/threonine-protein kinase SMG1, N-terminal / SMG1, PIKK catalytic domain / Serine/threonine-protein kinase smg-1 / Serine/threonine-protein kinase SMG1 N-terminal / Rapamycin binding domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / 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 / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Nonsense-mediated mRNA decay factor SMG8 / Serine/threonine-protein kinase SMG1 / Nonsense-mediated mRNA decay factor SMG9
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: 3.4 Å
データ登録者Langer LM / Conti E
資金援助 ドイツ, 1件
OrganizationGrant number国
Max Planck Society ドイツ
引用ジャーナル: Elife / 年: 2021
タイトル: Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8.
著者: Lukas M Langer / Fabien Bonneau / Yair Gat / Elena Conti /
要旨: The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 ...The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain. However, the molecular basis for this complex regulatory network has remained elusive. Here, we present cryo-electron microscopy reconstructions of human SMG1-9 and SMG1-8-9 complexes bound to either a SMG1 inhibitor or a non-hydrolyzable ATP analog at overall resolutions ranging from 2.8 to 3.6 Å. These structures reveal the basis with which a small molecule inhibitor preferentially targets SMG1 over other PIKKs. By comparison with our previously reported substrate-bound structure (Langer et al.,2020), we show that the SMG1 insertion domain can exert an autoinhibitory function by directly blocking the substrate-binding path as well as overall access to the SMG1 kinase active site. Together with biochemical analysis, our data indicate that SMG1 autoinhibition is stabilized by the presence of SMG8. Our results explain the specific inhibition of SMG1 by an ATP-competitive small molecule, provide insights into regulation of its kinase activity within the NMD pathway, and expand the understanding of PIKK regulatory mechanisms in general.
履歴
登録2021年10月6日-
ヘッダ(付随情報) 公開2021年12月1日-
マップ公開2021年12月1日-
更新2021年12月1日-
現状2021年12月1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: 0.3
  • 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: 0.3
  • 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-7pw5
  • 表面レベル: 0.3
  • 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_13675.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_13675.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
投影像・断面図

画像のコントロール

大きさ
明度
コントラスト
その他
軸Z (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å

表面

投影像

断面 (1/3)

断面 (1/2)

断面 (2/3)

画像は Spider により作成

ボクセルのサイズX=Y=Z: 0.8512 Å
密度

ヒストグラム

ヒストグラム (対数)
表面レベル登録者による: 0.24 / ムービー #1: 0.3
最小 - 最大-0.9302966 - 2.1141098
平均 (標準偏差)0.0072394293 (±0.05753046)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ384384384
Spacing384384384
セルA=B=C: 326.86078 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z0.851200520833330.851200520833330.85120052083333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z326.861326.861326.861
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.9302.1140.007

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添付データ

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試料の構成要素

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全体 : SMG1-SMG8-SMG9 kinase complex bound to a SMG1 inhibitor

全体名称: SMG1-SMG8-SMG9 kinase complex bound to a SMG1 inhibitor
要素
  • 複合体: SMG1-SMG8-SMG9 kinase complex bound to a SMG1 inhibitor
    • タンパク質・ペプチド: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
    • タンパク質・ペプチド: Protein SMG8
    • タンパク質・ペプチド: Protein SMG9
  • リガンド: INOSITOL HEXAKISPHOSPHATEフィチン酸
  • リガンド: 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea
  • リガンド: ADENOSINE-5'-TRIPHOSPHATE
  • リガンド: MAGNESIUM ION

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超分子 #1: SMG1-SMG8-SMG9 kinase complex bound to a SMG1 inhibitor

超分子名称: SMG1-SMG8-SMG9 kinase complex bound to a SMG1 inhibitor
タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3
由来(天然)生物種: Homo sapiens (ヒト)
組換発現生物種: Homo sapiens (ヒト)
分子量理論値: 597 KDa

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分子 #1: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-p...

分子名称: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: non-specific serine/threonine protein kinase
由来(天然)生物種: Homo sapiens (ヒト)
分子量理論値: 397.395375 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)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(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)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)FSTNF RDTVDILVGW HIDHTQKPSL TQQVSGWLQS LEPFWVADLA FSTTLLGQFL EDMEAYAEDL SHVAS GESV DEDVPPPSVS LPKLAALLRV FSTVVRSIGE RFSPIRGPPI TEAYVTDVLY RVMRCVTAAN QVFFSEAVLT AANECV GVL LGSLDPSMTI HCDMVITYGL DQLENCQTCG TDYIISVLNL LTLIVEQINT KLPSSFVEKL FIPSSKLLFL RYHKEKE VV AVAHAVYQAV LSLKNIPVLE TAYKLILGEM TCALNNLLHS LQLPEACSEI KHEAFKNHVF NVDNAKFVVI FDLSALTT I GNAKNSLIGM WALSPTVFAL LSKNLMIVHS DLAVHFPAIQ YAVLYTLYSH CTRHDHFISS SLSSSSPSLF DGAVISTVT TATKKHFSII LNLLGILLKK DNLNQDTRKL LMTWALEAAV LMRKSETYAP LFSLPSFHKF CKGLLANTLV EDVNICLQAC SSLHALSSS LPDDLLQRCV DVCRVQLVHS GTRIRQAFGK LLKSIPLDVV LSNNNHTEIQ EISLALRSHM SKAPSNTFHP Q DFSDVISF ILYGNSHRTG KDNWLERLFY SCQRLDKRDQ STIPRNLLKT DAVLWQWAIW EAAQFTVLSK LRTPLGRAQD TF QTIEGII RSLAAHTLNP DQDVSQWTTA DNDEGHGNNQ LRLVLLLQYL ENLEKLMYNA YEGCANALTS PPKVIRTFFY TNR QTCQDW LTRIRLSIMR VGLLAGQPAV TVRHGFDLLT EMKTTSLSQG NELEVTIMMV VEALCELHCP EAIQGIAVWS SSIV GKNLL WINSVAQQAE GRFEKASVEY QEHLCAMTGV DCCISSFDKS VLTLANAGRN SASPKHSLNG ESRKTVLSKP TDSSP EVIN YLGNKACECY ISIADWAAVQ EWQNSIHDLK KSTSSTSLNL KADFNYIKSL SSFESGKFVE CTEQLELLPG ENINLL AGG SKEKIDMKKL LPNMLSPDPR ELQKSIEVQL LRSSVCLATA LNPIEQDQKW QSITENVVKY LKQTSRIAIG PLRLSTL TV SQSLPVLSTL QLYCSSALEN TVSNRLSTED CLIPLFSEAL RSCKQHDVRP WMQALRYTMY QNQLLEKIKE QTVPIRSH L MELGLTAAKF ARKRGNVSLA TRLLAQCSEV QLGKTTTAQD LVQHFKKLST QGQVDEKWGP ELDIEKTKLL YTAGQSTHA MEMLSSCAIS FCKSVKAEYA VAKSILTLAK WIQAEWKEIS GQLKQVYRAQ HQQNFTGLST LSKNILTLIE LPSVNTMEEE YPRIESEST VHIGVGEPDF ILGQLYHLSS VQAPEVAKSW AALASWAYRW GRKVVDNAS(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)EGVIKVW RKVVDRIFSL YKLSCSAYFT FLKLNAGQIP LDEDDPRLHL SHRVEQSTDD MIV MATLRL LRLLVKHAGE LRQYLEHGLE TTPTAPWRGI IPQLFSRLNH PEVYVRQSIC NLLCRVAQDS PHLILYPAIV GTIS LSSES QASGNKFSTA IPTLLGNIQG EELLVSECEG GSPPASQDSN KDEPKSGLNE DQAMMQDCYS KIVDKLSSAN PTMVL QVQM LVAELRRVTV LWDELWLGVL LQQHMYVL(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)PHE KW FQDNYGD AIENALEKLK (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)YILRLEE ISPWLAAMTN TEIALPGEVS ARDTVTIHSV GGTITILPTK TKPKKLLFLG SDGKSYPY L FKGLEDLHLD ERIMQFLSIV NTMFATINRQ ETPRFHARHY SVTPLGTRSG LIQWVDGATP LFGLYKRWQQ REAALQAQK AQDSYQTPQN PGIVPRPSEL YYSKIGPALK TVGLSLDVSR RDWPLHVMKA VLEELMEATP PNLLAKELWS SCTTPDEWWR VTQSYARST AVMSMVGYII GLGDRHLDNV LIDMTTGEVV HIDYNVCFEK GKSLRVPEKV PFRMTQNIET ALGVTGVEGV F RLSCEQVL HIMRRGRETL LTLLEAFVYD PLVDWTAGGE AGFAGAVYGG GGQQAESKQS KREMEREITR SLFSSRVAEI KV NWFKNRD EMLVVLPKLD GSLDEYLSLQ EQLTDVEKLQ GKLLEEIEFL EGAEGVDHPS HTLQHRYSEH TQLQTQQRAV QEA IQVKLN EFEQWITHYQ AAFNNLEATQ LASLLQEIST QMDLGPPSYV PATAFLQNAG QAHLISQCEQ LEGEVGALLQ QRRS VLRGC LEQLHHYATV ALQYPKAIFQ KHRIEQWKTW MEELICNTTV ERCQELYRKY EMQYAPQPPP TVCQFITATE MTLQR YAAD INSRLIRQVE RLKQEAVTVP VCEDQLKEIE RCIKVFLHEN GEEGSLSLAS VIISALCTLT RRNLMMEGAA SSAGEQ LVD LTSRDGAWFL EELCSMSGNV TCLVQLLKQC HLVPQDLDIP NPMEASETVH LANGVYTSLQ ELNSNFRQII FPEALRC LM KGEYTLESML HELDGLIEQT TDGVPLQTLV ESLQAYLRNA AMGLEEETHA HYIDVARLLH AQYGELIQPR NGSVDETP K MSAGQMLLVA FDGMFAQVET AFSLLVEKLN KMEIPIAWRK IDIIREARST QVNFFDDDNH RQVLEEIFFL KRLQTIKEF FRLCGTFSKT LSGSSSLEDQ NTVNGPVQIV NVKTLFRNSC FSEDQMAKPI KAFTADFVRQ LLIGLPNQAL GLTLCSFISA LGVDIIAQV EAKDFGAESK VSVDDLCKKA VEHNIQIGKF SQLVMNRATV LASSYDTAWK KHDLVRRLET SISSCKTSLQ R VQLHIAMF QWQHEDLLIN RPQAMSVTPP PRSAILTSMK KKLHTLSQIE TSIATVQEKL AALESSIEQR LKWAGGANPA LA PVLQDFE ATIAERRNLV LKESQRASQV TFLCSNIIHF ESLRTRTAEA LNLDAALFEL IKRCQQMCSF ASQFNSSVSE LEL RLLQRV DTGLEHPIGS SEWLLSAHKQ LTQDMSTQRA IQTEKEQQIE TVCETIQNLV DNIKTVLTGH NRQLGDVKHL LKAM AKDEE AALADGEDVP YENSVRQFLG EYKSWQDNIQ TVLFTLVQAM GQVRSQEHVE MLQEITPTLK ELKTQSQSIY NNLVS FASP LVTDATNECS SPTSSATYQP SFAAAVRSNT GQKTQPDVMS QNARKLIQKN LATSADTPPS TVPGTGKSVA CSPKKA VRD PKTGKAVQER NSYAVSVWKR VKAKLEGRDV DPNRRMSVAE QVDYVIKEAT NLDNLAQLYE GWTAWV

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分子 #2: Protein SMG8

分子名称: Protein SMG8 / 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: 109.82575 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: MAGPVSLRDL LMGASAWMGS ESPGGSPTEG GGSAAGGPEP PWREDEICVV GIFGKTALRL NSEKFSLVNT VCDRQVFPLF RHQDPGDPG PGIRTEAGAV GEAGGAEDPG AAAGGSVRGS GAVAEGNRTE AGSQDYSLLQ AYYSQESKVL YLLLTSICDN S QLLRACRA ...文字列:
MAGPVSLRDL LMGASAWMGS ESPGGSPTEG GGSAAGGPEP PWREDEICVV GIFGKTALRL NSEKFSLVNT VCDRQVFPLF RHQDPGDPG PGIRTEAGAV GEAGGAEDPG AAAGGSVRGS GAVAEGNRTE AGSQDYSLLQ AYYSQESKVL YLLLTSICDN S QLLRACRA LQSGEAGGGL SLPHAEAHEF WKHQEKLQCL SLLYLFSVCH ILLLVHPTCS FDITYDRVFR ALDGLRQKVL PL LKTAIKD CPVGKDWKLN CRPCPPRLLF LFQLNGALKV EPPRNQDPAH PDKPKKHSPK RRLQHALEDQ IYRIFRKSRV LTN QSINCL FTVPANQAFV YIVPGSQEED PVGMLLDQLR SHCTVKDPES LLVPAPLSGP RRYQVMRQHS RQQLSFHIDS SSSS SSGQL VDFTLREFLW QHVELVLSKK GFDDSVGRNP QPSHFELPTY QKWISAASKL YEVAIDGKEE DLGSPTGELT SKILS SIKV LEGFLDIDTK FSENRCQKAL PMAHSAYQSN LPHNYTMTVH KNQLAQALRV YSQHARGPAF HKYAMQLHED CYKFWS NGH QLCEERSLTD QHCVHKFHSL PKSGEKPEAD RNPPVLYHNS RARSTGACNC GRKQAPRDDP FDIKAANYDF YQLLEEK CC GKLDHINFPV FEPSTPDPAP AKNESSPAPP DSDADKLKEK EPQTQGESTS LSLALSLGQS TDSLGTYPAD PQAGGDNP E VHGQVEVKTE KRPNFVDRQA STVEYLPGML HSNCPKGLLP KFSSWSLVKL GPAKSYNFHT GLDQQGFIPG TNYLMPWDI VIRTRAEDEG DLDTNSWPAP NKAIPGKRSA VVMGRGRRRD DIARAFVGFE YEDSRGRRFM CSGPDKVMKV MGSGPKESAL KALNSDMPL YILSSSQGRG LKPHYAQLMR LFVVVPDAPL QIILMPQVQP GPPPCPVFYP EKQEITLPPD GLWVLRFPYA Y VTERGPCF PPKENVQLMS YKVLRGVLKA VTQ

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分子 #3: Protein SMG9

分子名称: Protein SMG9 / 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: 57.717473 KDa
組換発現生物種: Homo sapiens (ヒト)
配列文字列: MSESGHSQPG LYGIERRRRW KEPGSGGPQN LSGPGGRERD YIAPWERERR DASEETSTSV MQKTPIILSK PPAERSKQPP PPTAPAAPP APAPLEKPIV LMKPREEGKG PVAVTGASTP EGTAPPPPAA PAPPKGEKEG QRPTQPVYQI QNRGMGTAAP A AMDPVVGQ ...文字列:
MSESGHSQPG LYGIERRRRW KEPGSGGPQN LSGPGGRERD YIAPWERERR DASEETSTSV MQKTPIILSK PPAERSKQPP PPTAPAAPP APAPLEKPIV LMKPREEGKG PVAVTGASTP EGTAPPPPAA PAPPKGEKEG QRPTQPVYQI QNRGMGTAAP A AMDPVVGQ AKLLPPERMK HSIKLVDDQM NWCDSAIEYL LDQTDVLVVG VLGLQGTGKS MVMSLLSANT PEEDQRTYVF RA QSAEMKE RGGNQTSGID FFITQERIVF LDTQPILSPS ILDHLINNDR KLPPEYNLPH TYVEMQSLQI AAFLFTVCHV VIV VQDWFT DLSLYRFLQT AEMVKPSTPS PSHESSSSSG SDEGTEYYPH LVFLQNKARR EDFCPRKLRQ MHLMIDQLMA HSHL RYKGT LSMLQCNVFP GLPPDFLDSE VNLFLVPFMD SEAESENPPR AGPGSSPLFS LLPGYRGHPS FQSLVSKLRS QVMSM ARPQ LSHTILTEKN WFHYAARIWD GVRKSSALAE YSRLLA

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分子 #4: INOSITOL HEXAKISPHOSPHATE

分子名称: INOSITOL HEXAKISPHOSPHATE / タイプ: ligand / ID: 4 / 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 / フィチン酸

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分子 #5: 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimid...

分子名称: 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea
タイプ: ligand / ID: 5 / コピー数: 1 / 式: 88C
分子量理論値: 566.074 Da
Chemical component information

ChemComp-88C:
1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea

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分子 #6: ADENOSINE-5'-TRIPHOSPHATE

分子名称: ADENOSINE-5'-TRIPHOSPHATE / タイプ: ligand / ID: 6 / コピー数: 1 / 式: ATP
分子量理論値: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP / ATP, エネルギー貯蔵分子*YM / アデノシン三リン酸

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分子 #7: MAGNESIUM ION

分子名称: MAGNESIUM ION / タイプ: ligand / ID: 7 / コピー数: 1 / 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-PROPANE

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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: GATAN K3 (6k x 4k) / 平均電子線量: 89.32 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 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 角度割当タイプ: MAXIMUM LIKELIHOOD
最終 再構成解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 114269

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る