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- EMDB-6816: NuA4 TEEAA sub-complex -

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基本情報

登録情報
データベース: EMDB / ID: EMD-6816
タイトルNuA4 TEEAA sub-complex
マップデータ
試料
  • 複合体: NuA4 TEEAA sub-complex
    • タンパク質・ペプチド: Transcription-associated protein 1
    • タンパク質・ペプチド: Chromatin modification-related protein EAF1
    • タンパク質・ペプチド: Eaf1-disorder domain
    • タンパク質・ペプチド: Chromatin modification-related protein EAF5
    • タンパク質・ペプチド: Transcription-associated protein 1
    • タンパク質・ペプチド: Actin-related protein 4
    • タンパク質・ペプチド: Actin
    • タンパク質・ペプチド: Chromatin modification-related protein EAF1
機能・相同性
機能・相同性情報


RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / SLIK (SAGA-like) complex / kinetochore assembly ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / SLIK (SAGA-like) complex / kinetochore assembly / Ino80 complex / SAGA complex / SWI/SNF complex / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / protein secretion / Ub-specific processing proteases / actin filament / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / structural constituent of cytoskeleton / endocytosis / chromatin organization / histone binding / protein-containing complex assembly / hydrolase activity / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / cytosol
類似検索 - 分子機能
Chromatin modification-related protein EAF5 / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain ...Chromatin modification-related protein EAF5 / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Homeobox-like domain superfamily / ATPase, nucleotide binding domain / Armadillo-type fold / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Transcription-associated protein 1 / Chromatin modification-related protein EAF5 / Actin / Actin-related protein 4 / Chromatin modification-related protein EAF1
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Baker's yeast (パン酵母) / 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 / ネガティブ染色法 / 解像度: 4.7 Å
データ登録者Wang X / Cai G
資金援助 中国, 3件
OrganizationGrant number国
National Basic Research Program2014CB910700 中国
the National Natural Science Foundation of China31170694 中国
the National Natural Science Foundation of China31570726 中国
引用ジャーナル: Nat Commun / 年: 2018
タイトル: Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex.
著者: Xuejuan Wang / Salar Ahmad / Zhihui Zhang / Jacques Côté / Gang Cai /
要旨: The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and ...The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and regulatory mechanism. Here, we report the 4.7 Å cryo-electron microscopy (cryo-EM) structure of a NuA4/TIP60 TEEAA assembly (Tra1, Eaf1, Eaf5, actin and Arp4) and the 7.6 Å cryo-EM structure of a TEEAA-piccolo assembly (Esa1, Epl1, Yng2 and Eaf6). The Tra1 and Eaf1 constitute the assembly scaffold. The Eaf1 SANT domain tightly binds to the LBE and FATC domains of Tra1 by ionic interactions. The actin/Arp4 peripherally associates with Eaf1 HSA domain. The Eaf5/7/3 (TINTIN) and piccolo modules largely pack against the FAT and HEAT repeats of Tra1 and their association depends on Eaf1 N-terminal and HSA regions, respectively. These structures elucidate the detailed architecture and molecular interactions between NuA4 subunits and offer exciting insights into the scaffolding and regulatory mechanisms of Tra1 pseudokinase.
履歴
登録2017年8月18日-
ヘッダ(付随情報) 公開2018年4月18日-
マップ公開2018年4月18日-
更新2019年11月6日-
現状2019年11月6日処理サイト: PDBj / 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: 0.0225
  • 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: 0.0225
  • 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-5y81
  • 表面レベル: 0.0225
  • 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_6816.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_6816.map.gz / 形式: CCP4 / 大きさ: 91.1 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.)
1.3 Å/pix.
x 288 pix.
= 374.4 Å		1.3 Å/pix.
x 288 pix.
= 374.4 Å		1.3 Å/pix.
x 288 pix.
= 374.4 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: 1.3 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: 0.0225 / ムービー #1: 0.0225
最小 - 最大-0.062639356 - 0.13194954
平均 (標準偏差)0.00026157088 (±0.005168174)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ288288288
Spacing288288288
セルA=B=C: 374.4 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0630.1320.000

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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 : NuA4 TEEAA sub-complex

全体名称: NuA4 TEEAA sub-complex
要素
  • 複合体: NuA4 TEEAA sub-complex
    • タンパク質・ペプチド: Transcription-associated protein 1
    • タンパク質・ペプチド: Chromatin modification-related protein EAF1
    • タンパク質・ペプチド: Eaf1-disorder domain
    • タンパク質・ペプチド: Chromatin modification-related protein EAF5
    • タンパク質・ペプチド: Transcription-associated protein 1
    • タンパク質・ペプチド: Actin-related protein 4
    • タンパク質・ペプチド: Actin
    • タンパク質・ペプチド: Chromatin modification-related protein EAF1

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超分子 #1: NuA4 TEEAA sub-complex

超分子名称: NuA4 TEEAA sub-complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all
由来(天然)生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c

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分子 #1: Transcription-associated protein 1

分子名称: Transcription-associated protein 1 / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 130.470539 KDa
配列文字列: YNAWYQSINI LESIQSNTSI DNTKIIEANE DALLELYVNL QEEDMFYGLW RRRAKYTETN IGLSYEQIGL WDKAQQLYEV AQVKARSGA LPYSQSEYAL WEDNWIQCAE KLQHWDVLTE LAKHEGFTDL LLECGWRVAD WNSDRDALEQ SVKSVMDVPT P RRQMFKTF ...文字列:
YNAWYQSINI LESIQSNTSI DNTKIIEANE DALLELYVNL QEEDMFYGLW RRRAKYTETN IGLSYEQIGL WDKAQQLYEV AQVKARSGA LPYSQSEYAL WEDNWIQCAE KLQHWDVLTE LAKHEGFTDL LLECGWRVAD WNSDRDALEQ SVKSVMDVPT P RRQMFKTF LALQNFAESR KGDQEVRKLC DEGIQLSLIK WVSLPIRYTP AHKWLLHGFQ QYMEFLEATQ IYANLHTTTV QN LDSKAQE IKRILQAWRD RLPNTWDDVN MWNDLVTWRQ HAFQVINNAY LPLIPALQQS NSNSNINTHA YRGYHEIAWV INR FAHVAR KHNMPDVCIS QLARIYTLPN IEIQEAFLKL REQAKCHYQN MNELTTGLDV ISNTNLVYFG TVQKAEFFTL KGMF LSKLR AYEEANQAFA TAVQIDLNLA KAWAQWGFFN DRRLSEEPNN ISFASNAISC YLQAAGLYKN SKIRELLCRI LWLIS IDDA SGMLTNAFDS FRGEIPVWYW ITFIPQLLTS LSHKEANMVR HILIRIAKSY PQALHFQLRT TKEDFAVIQR QTMAVM GDK PDTNDRNGRR QPWEYLQELN NILKTAYPLL ALSLESLVAQ INDRFKSTTD EDLFRLINVL LIDGTLNYNR LPFPRKN PK LPENTEKNLV KFSTTLLAPY IRPKFNADFI DNKPDYETYI KRLRYWRRRL ENKLDRASKK ENLEVLCPHL SNFHHQKF E DIEIPGQYLL NKDNNVHFIK IARFLPTVDF VRGTHSSYRR LMIRGHDGSV HSFAVQYPAV RHSRREERMF QLYRLFNKS LSKNVETRRR SIQFNLPIAI PLSPQVRIMN DSVSFTTLHE IHNEFCKKKG FDPDDIQDFM ADKLNAAHDD ALPAPDMTIL KVEIFNSIQ TMFVPSNVLK DHFTSLFTQF EDFWLFRKQF ASQYSSFVFM SYMMMINNRT PHKIHVDKTS GNVFTLEMLP S RFPYERVK PLLKNHDLSL PPDSPIFHNN EPVPFRLTPN IQSLIGDSAL EGIFAVNLFT ISRALIEPDN ELNTYLALFI RD EIISWFS NLHRPIIENP QLREMVQTNV DLIIRKVAQL GHLNSTPTVT TQFILDCIGS AVSPRNLART DVNFMPWF

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分子 #2: Chromatin modification-related protein EAF1

分子名称: Chromatin modification-related protein EAF1 / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 39.431434 KDa
配列文字列: PTIWLSEDDQ ELVKNINTYG YNWELISAHM THRLTYSYLS NIERRTPWQC FERFVQLNER FNFSDLKGPR AHSAQQWLIE AHKFQQRQN RRISPLGVNT ESIQRGHRRL RWASMFEAIR KCMKKRENTP RPNPTQPRKP LDCKNMKVPT PAEMSLLKAQ R DEALRRDI ...文字列:
PTIWLSEDDQ ELVKNINTYG YNWELISAHM THRLTYSYLS NIERRTPWQC FERFVQLNER FNFSDLKGPR AHSAQQWLIE AHKFQQRQN RRISPLGVNT ESIQRGHRRL RWASMFEAIR KCMKKRENTP RPNPTQPRKP LDCKNMKVPT PAEMSLLKAQ R DEALRRDI QLRRTVKNRL QQRQQQSQQA HSSRAQSPIP SNGKSSSNLA RNGQASAPRP NQKQYTEQDI IESYSRKLLE QK PDIGPEM ALKAAKNYYR TLREQQQQLK QHQIQQQRQQ LQEESSHVQQ LQQLQPGSQA PPPKSSPSQS SLSNISNINS APR IKSPTP QEILQRFQKQ

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分子 #3: Eaf1-disorder domain

分子名称: Eaf1-disorder domain / 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: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 42.570492 KDa
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)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(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: Chromatin modification-related protein EAF5

分子名称: Chromatin modification-related protein EAF5 / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 31.689264 KDa
配列文字列: MDKEVSELVV LQLIHTLISN KNEELVRNGG GINMIGNNLR ISLVKLTNEI QNNLLINELT NLRRQSNVAN GNRKLGINDI LTIVKNLFP EYRTTLNDGQ LSLHGLEMHD IEKLLDEKYD RFKKTQVEQI RMMEDEILKN GIKTGASQLQ PHANAGKSGS A GTSATITT ...文字列:
MDKEVSELVV LQLIHTLISN KNEELVRNGG GINMIGNNLR ISLVKLTNEI QNNLLINELT NLRRQSNVAN GNRKLGINDI LTIVKNLFP EYRTTLNDGQ LSLHGLEMHD IEKLLDEKYD RFKKTQVEQI RMMEDEILKN GIKTGASQLQ PHANAGKSGS A GTSATITT TTPHMAHSMD PKREKLLKLY RDTVLNKLES KTGNFQKLFK SPDGSIIKNE INYEDIKNET PGSVHELQLI LQ KSITDGV MRKVIGTDDW KLARQVQFEL DDTVQFMRRA LE

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分子 #5: Transcription-associated protein 1

分子名称: Transcription-associated protein 1 / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 303.020531 KDa
配列文字列: MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG ...文字列:
MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG DLDSPKEPQA DELLDEFSKN DEEKDFPSKQ SSTEPRFENS TSSNGLRSSM FSFKILSECP ITMVTLYSSY KQ LTSTSLP EFTPLIMNLL NIQIKQQQEA REQAESRGEH FTSISTEIIN RPAYCDFILA QIKATSFLAY VFIRGYAPEF LQD YVNFVP DLIIRLLQDC PSELSSARKE LLHATRHILS TNYKKLFLPK LDYLFDERIL IGNGFTMHET LRPLAYSTVA DFIH NIRSE LQLSEIEKTI KIYTGYLLDE SLALTVQIMS AKLLLNLVER ILKLGKENPQ EAPRAKKLLM IIIDSYMNRF KTLNR QYDT IMKYYGRYET HKKEKAEKLK NSIQDNDKES EEFMRKVLEP SDDDHLMPQP KKEDINDSPD VEMTESDKVV KNDVEM FDI KNYAPILLLP TPTNDPIKDA FYLYRTLMSF LKTIIHDLKV FNPPPNEYTV ANPKLWASVS RVFSYEEVIV FKDLFHE CI IGLKFFKDHN EKLSPETTKK HFDISMPSLP VSATKDAREL MDYLAFMFMQ MDNATFNEII EQELPFVYER MLEDSGLL H VAQSFLTSEI TSPNFAGILL RFLKGKLKDL GNVDFNTSNV LIRLFKLSFM SVNLFPNINE VVLLPHLNDL ILNSLKYST TAEEPLVYFY LIRTLFRSIG GGRFENLYRS IKPILQVLLQ SLNQMILTAR LPHERELYVE LCITVPVRLS VLAPYLPFLM KPLVFALQQ YPDLVSQGLR TLELCIDNLT AEYFDPIIEP VIDDVSKALF NLLQPQPFNH AISHNVVRIL GKLGGRNRQF L KPPTDLTE KTELDIDAIA DFKINGMPED VPLSVTPGIQ SALNILQSYK SDIHYRKSAY KYLTCVLLLM TKSSAEFPTN YT ELLKTAV NSIKLERIGI EKNFDLEPTV NKRDYSNQEN LFLRLLESVF YATSIKELKD DAMDLLNNLL DHFCLLQVNT TLL NKRNYN GTFNIDLKNP NFMLDSSLIL DAIPFALSYY IPEVREVGVL AYKRIYEKSC LIYGEELALS HSFIPELAKQ FIHL CYDET YYNKRGGVLG IKVLIDNVKS SSVFLKKYQY NLANGLLFVL KDTQSEAPSA ITDSAEKLLI DLLSITFADV KEEDL GNKV LENTLTDIVC ELSNANPKVR NACQKSLHTI SNLTGIPIVK LMDHSKQFLL SPIFAKPLRA LPFTMQIGNV DAITFC LSL PNTFLTFNEE LFRLLQESIV LADAEDESLS TNIQKTTEYS TSEQLVQLRI ACIKLLAIAL KNEEFATAQQ GNIRIRI LA VFFKTMLKTS PEIINTTYEA LKGSLAENSK LPKELLQNGL KPLLMNLSDH QKLTVPGLDA LSKLLELLIA YFKVEIGR K LLDHLTAWCR VEVLDTLFGQ DLAEQMPTKI IVSIINIFHL LPPQADMFLN DLLLKVMLLE RKLRLQLDSP FRTPLARYL NRFHNPVTEY FKKNMTLRQL VLFMCNIVQR PEAKELAEDF EKELDNFYDF YISNIPKNQV RVVSFFTNMV DLFNTMVITN GDEWLKKKG NMILKLKDML NLTLKTIKEN SFYIDHLQLN QSIAKFQALY LRFTELSERD QNPLLLDFID FSFSNGIKAS Y SLKKFIFH NIIASSNKEK QNNFINDATL FVLSDKCLDA RIFVLKNVIN STLIYEVATS GSLKSYLVED KKPKWLELLH NK IWKNSNA ILAYDVLDHH DLFRFELLQL SAIFIKADPE IIAEIKKDII KFCWNFIKLE DTLIKQSAYL VTSYFISKFD FPI KVVTQV FVALLRSSHV EARYLVKQSL DVLTPVLHER MNAAGTPDTW INWVKRVMVE NSSSQNNILY QFLISHPDLF FNSR DLFIS NIIHHMNKIT FMSNSNSDSH TLAIDLASLI LYWENKTLEI TNVNNTKTDS DGDVVMSDSK SDINPVEADT TAIIV DANN NSPISLHLRE ACTAFLIRYV CASNHRAIET ELGLRAINIL SELISDKHWT NVNVKLVYFE KFLIFQDLDS ENILYY CMN ALDVLYVFFK NKTKEWIMEN LPTIQNLLEK CIKSDHHDVQ EALQKVLQVI MKAIKAQGVS VIIEEESPGK TFIQMLT SV ITQDLQETSS VTAGVTLAWV LFMNFPDNIV PLLTPLMKTF SKLCKDHLSI SQPKDAMALE EARITTKLLE KVLYILSL K VSLLGDSRRP FLSTVALLID HSMDQNFLRK IVNMSRSWIF NTEIFPTVKE KAAILTKMLA FEIRGEPSLS KLFYEIVLK LFDQEHFNNT EITVRMEQPF LVGTRVEDIG IRKRFMTILD NSLERDIKER LYYVIRDQNW EFIADYPWLN QALQLLYGSF NREKELSLK NIYCLSPPSI LQEYLPENAE MVTEVNDLEL SNFVKGHIAS MQGLCRIISS DFIDSLIEIF YQDPKAIHRA W VTLFPQVY KSIPKNEKYG FVRSIITLLS KPYHTRQISS RTNVINMLLD SISKIESLEL PPHLVKYLA

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分子 #6: Actin-related protein 4

分子名称: Actin-related protein 4 / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 54.991797 KDa
配列文字列: PMSNAALQVY GGDEVSAVVI DPGSYTTNIG YSGSDFPQSI LPSVYGKYTA DEGNKKIFSE QSIGIPRKDY ELKPIIENGL VIDWDTAQE QWQWALQNEL YLNSNSGIPA LLTEPVWNST ENRKKSLEVL LEGMQFEACY LAPTSTCVSF AAGRPNCLVV D IGHDTCSV ...文字列:
PMSNAALQVY GGDEVSAVVI DPGSYTTNIG YSGSDFPQSI LPSVYGKYTA DEGNKKIFSE QSIGIPRKDY ELKPIIENGL VIDWDTAQE QWQWALQNEL YLNSNSGIPA LLTEPVWNST ENRKKSLEVL LEGMQFEACY LAPTSTCVSF AAGRPNCLVV D IGHDTCSV SPIVDGMTLS KSTRRNFIAG KFINHLIKKA LEPKEIIPLF AIKQRKPEFI KKTFDYEVDK SLYDYANNRG FF QECKETL CHICPTKTLE ETKTELSSTA KRSIESPWNE EIVFDNETRY GFAEELFLPK EDDIPANWPR SNSGVVKTWR NDY VPLKRT KPSGVNKSDK KVTPTEEKEQ EAVSKSTSPA ANSADTPNET GKRPLEEEKP PKENNELIGL ADLVYSSIMS SDVD LRATL AHNVVLTGGT SSIPGLSDRL MTELNKILPS LKFRILTTGH TIERQYQSWL GGSILTSLGT FHQLWVGKKE YEEVG VERL LNDRFR

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分子 #7: Actin

分子名称: Actin / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 41.735547 KDa
配列文字列: MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG ...文字列:
MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG FSLPHAILRI DLAGRDLTDY LMKILSERGY SFSTTAEREI VRDIKEKLCY VALDFEQEMQ TAAQSSSIEK SY ELPDGQV ITIGNERFRA PEALFHPSVL GLESAGIDQT TYNSIMKCDV DVRKELYGNI VMSGGTTMFP GIAERMQKEI TAL APSSMK VKIIAPPERK YSVWIGGSIL ASLTTFQQMW ISKQEYDESG PSIVHHKCF

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分子 #8: Chromatin modification-related protein EAF1

分子名称: Chromatin modification-related protein EAF1 / 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: Baker's yeast (パン酵母) / 株: ATCC 204508 / S288c
分子量理論値: 4.882613 KDa
配列文字列:
THQNILLEEA KWMQADFKEG HKYKVAICTA MAQAIKDYWT Y

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実験情報

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構造解析

手法ネガティブ染色法, 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: 8
染色タイプ: NONE / 材質: Uranyl Formate
凍結凍結剤: ETHANE

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
撮影フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
平均電子線量: 30.0 e/Å2
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 FIELD
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

最終 再構成解像度のタイプ: BY AUTHOR / 解像度: 4.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 63197
初期 角度割当タイプ: PROJECTION MATCHING
最終 角度割当タイプ: PROJECTION MATCHING

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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