[日本語] English
万見
- PDB-6o22: Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine ace... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6o22
タイトルStructure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate.
要素
  • Histone H3.2
  • Histone H4ヒストンH4
  • Histone acetyltransferase RTT109
  • Histone chaperone ASF1
  • Vacuolar protein sorting-associated protein 75液胞
キーワードCHAPERONE (シャペロン)
機能・相同性
機能・相同性情報


: / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA ...: / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / retrotransposon silencing / DNA replication-dependent chromatin assembly / nucleosome disassembly / histone H3 acetyltransferase activity / : / histone H3K27 acetyltransferase activity / silent mating-type cassette heterochromatin formation / peptide-lysine-N-acetyltransferase activity / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / ヒストンアセチルトランスフェラーゼ / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / ヌクレオソーム / nucleosome assembly / protein transport / chromatin organization / histone binding / 遺伝子発現の調節 / chromosome, telomeric region / protein heterodimerization activity / DNA damage response / chromatin binding / クロマチン / regulation of transcription by RNA polymerase II / DNA binding / 核質 / identical protein binding / 細胞核 / 細胞質基質
類似検索 - 分子機能
Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone ...Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / ヒストンH4 / ヒストンH4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / ヒストンH3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / サンドイッチ / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Histone chaperone ASF1 / Vacuolar protein sorting-associated protein 75 / ヒストンH4 / Histone H3.2 / Histone acetyltransferase RTT109
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
Xenopus laevis (アフリカツメガエル)
手法溶液NMR / 溶液散乱 / simulated annealing
データ登録者Danilenko, N. / Carlomagno, T. / Kirkpatrick, J.P.
引用ジャーナル: Nat Commun / 年: 2019
タイトル: Histone chaperone exploits intrinsic disorder to switch acetylation specificity.
著者: Nataliya Danilenko / Lukas Lercher / John Kirkpatrick / Frank Gabel / Luca Codutti / Teresa Carlomagno /
要旨: Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both ...Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.
履歴
登録2019年2月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年7月31日Provider: repository / タイプ: Initial release
改定 1.12019年8月14日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年5月1日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75
C: Histone acetyltransferase RTT109
D: Histone chaperone ASF1
E: Histone H3.2
F: Histone H4


分子量 (理論値)分子数
合計 (水以外)170,4786
ポリマ－170,4786
非ポリマー00
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration, light scattering
タイプ名称対称操作数
identity operation1_5551
Buried area18410 Å2
ΔGint-102 kcal/mol
Surface area57190 Å2
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)1 / 150structures with the least restraint violations
代表モデルモデル #1closest to the average

-
要素

#1: タンパク質 Vacuolar protein sorting-associated protein 75 / 液胞


分子量: 30656.084 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: VPS75, YNL246W, N0890 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P53853
#2: タンパク質 Histone acetyltransferase RTT109 / Regulator of Ty1 transposition protein 109


分子量: 50765.434 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RTT109, KIM2, REM50, YLL002W, L1377 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q07794, ヒストンアセチルトランスフェラーゼ
#3: タンパク質 Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


分子量: 31585.139 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: ASF1, CIA1, YJL115W, J0755 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P32447
#4: タンパク質 Histone H3.2 / Histone H3


分子量: 15421.101 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P84233
#5: タンパク質 Histone H4 / ヒストンH4


分子量: 11394.426 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62799

-
実験情報

-
実験

実験
手法
溶液NMR
溶液散乱
NMR実験
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDタイプ
111isotropic12D 1H-13C HSQC
122isotropic12D 1H-13C HSQC
133isotropic12D 1H-13C HSQC
144isotropic12D 1H-13C HSQC
155isotropic12D 1H-13C HSQC
166isotropic12D 1H-13C HSQC
177isotropic12D 1H-13C HSQC

-
試料調製

詳細
タイプSolution-ID内容Label溶媒系詳細
solution170 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4, 100% D2OVps75_in_FC_ILV100% D2O
solution270 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag, 70 uM H4, 100% D2Ocomplex_Vps75(ILV)_H3(63C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution390 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 90 uM Rtt109, 90 uM Asf1, 90 uM H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag, 90 uM H4, 100% D2Ocomplex_Vps75(ILV)_H3(76C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution430 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(30C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(30C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(30C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution570 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4(82C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(82C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(82C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution680 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 80 uM Rtt109, 80 uM Asf1, 80 uM H3, 80 uM H4(45C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(45C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(45C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C)
solution730 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(93C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(93C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(93C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C)
試料
濃度 (mg/ml)構成要素Isotopic labelingSolution-ID
70 uMVps75 (dimer)ILV methyl labelled, perdeuterated1
70 uMRtt109natural abundance1
70 uMAsf1natural abundance1
70 uMH3natural abundance1
70 uMH4natural abundance1
70 uMVps75 (dimer)ILV methyl labelled, perdeuterated2
70 uMRtt109natural abundance2
70 uMAsf1natural abundance2
70 uMH3(110A,63C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance2
70 uMH4natural abundance2
90 uMVps75 (dimer)ILV methyl labelled, perdeuterated3
90 uMRtt109natural abundance3
90 uMAsf1natural abundance3
90 uMH3(110A,76C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance3
90 uMH4natural abundance3
30 uMVps75 (dimer)ILV methyl labelled, perdeuterated4
30 uMRtt109natural abundance4
30 uMAsf1natural abundance4
30 uMH3natural abundance4
30 uMH4(30C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance4
70 uMVps75 (dimer)ILV methyl labelled, perdeuterated5
70 uMRtt109natural abundance5
70 uMAsf1natural abundance5
70 uMH3natural abundance5
70 uMH4(82C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance5
80 uMVps75 (dimer)ILV methyl labelled, perdeuterated6
80 uMRtt109natural abundance6
80 uMAsf1natural abundance6
80 uMH3natural abundance6
80 uMH4(45C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance6
30 uMVps75 (dimer)ILV methyl labelled, perdeuterated7
30 uMRtt109natural abundance7
30 uMAsf1natural abundance7
30 uMH3natural abundance7
30 uMH4(93C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance7
試料状態イオン強度: 150 mM / Label: cond_1 / pH: 6.5 / 圧: 1 atm / 温度: 298 K

-
データ収集

NMRスペクトロメータータイプ: Bruker AVANCE III / 製造業者: Bruker / モデル: AVANCE III / 磁場強度: 850 MHz
Soln scatter

Buffer name: 50 MM CITRATE, 150 MM NACL, 5MM BME IN 99.9% D2O / Data analysis software list: PRIMUS, GNOM / Sample pH: 6.5 / Source class: N / 温度: 298 K / タイプ: neutron

IDConc. range (mg/ml)Data reduction software list検出器タイプMean guiner radius (nm)Mean guiner radius esd (nm)Protein lengthSource beamline instrumentSource type
14.9ILL IN-HOUSE PACKAGE (GRASP)He multidetector 128 linear sensitive Reuter-Stokes detector2.840.0189.5D22ILL
22.35QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.530.03811.5KWS-1FRM2
33.85QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detectorKWS-1FRM2
43.8QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.280.04610.5KWS-1FRM2
54.7QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.50.04611KWS-1FRM2
65.2QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.060.07610.5KWS-1FRM2

-
解析

NMR software
名称開発者分類
CcpNMRCCPNデータ解析
HADDOCKBonvinstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax解析
TopSpinBruker Biospin解析
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman精密化
FuDAD. Flemming Hansenデータ解析
精密化手法: simulated annealing / ソフトェア番号: 5
代表構造選択基準: closest to the average
NMRアンサンブルコンフォーマー選択の基準: structures with the least restraint violations
計算したコンフォーマーの数: 150 / 登録したコンフォーマーの数: 1
Soln scatter model手法: X-RAY STRUCTURES OF THE SUBUNITS WERE DOCKED WITH HADDOCK-BASED M3 DOCKING PROTOCOL. DOCKING WAS GUIDED BY PRE DISTANCE RESTRAINTS, STRUCTURES WERE SELECTED BY FITNESS TO THE SANS DATA.
コンフォーマー選択の基準: BEST FITNESS TO THE SANS DATA, CLOSEST TO THE CLUSTER CENTER.
詳細: THE STRUCTURE WAS DETERMINED USING A HADDOCK-BASED M3 DOCKING PROTOCOL. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 3Q66, PDB ID 2HUE. PRE DISTANCE RESTRAINTS WERE ...詳細: THE STRUCTURE WAS DETERMINED USING A HADDOCK-BASED M3 DOCKING PROTOCOL. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 3Q66, PDB ID 2HUE. PRE DISTANCE RESTRAINTS WERE USED FOR STRUCTURE CALCULATION WITH HADDOCK-M3. 5000 STRUCTURES WERE CALCULATED DURING THE IT0 STAGE, 150 STRUCTURES WERE CALCULATED DURING THE IT1 STAGE. SANS DATA WERE USED FOR THE STRUCTURE SELECTION.
Entry fitting list: PDB ID 3Q66, PDB ID 2HUE / Num. of conformers calculated: 150 / Num. of conformers submitted: 1 / Software author list: KARACA, CARLOMAGNO, RODRIGUES, BONVIN / Software list: M3

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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