SASDBU7: DNA binding domain (DBD) of chromo domain-containing protein 1 (C...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDBU7

試料

DNA binding domain (DBD) of chromo domain-containing protein 1 (Chd1: 1009-1274)

• chromodomain helicase DNA binding domain (protein), Chd1-DBD, Saccharomyces cerevisiae

機能・相同性

分子機能:

nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / 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 / chromatin DNA binding / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus

ドメイン・相同性:

Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase

構成要素:

Chromo domain-containing protein 1

• 生物種: Saccharomyces cerevisiae (パン酵母)
• 引用: ジャーナル: Elife / 年: 2017; タイトル: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.; 著者: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Vijender Singh / Nicola Wiechens / Daniel P Ryan / Hassane El-Mkami / Maxim Petoukhov / Dmitri I Svergun / Barbara Treutlein / Salina Quack / Monika Fischer / Jens Michaelis / Bettina Böttcher / David G Norman / Tom Owen-Hughes / ; 要旨: The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.

登録者

• Ramasubramanian Sundaramoorthy (University of Dundee, Dundee, UK)

モデル

• モデル #919: ; タイプ: dummy / ソフトウェア: GASBOR (2.3i) / ダミー原子の半径: 1.90 A / 対称性: C1 / カイ2乗値: 2.10; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: DNA binding domain (DBD) of chromo domain-containing protein 1 (Chd1: 1009-1274); 試料濃度: 1.20-9.90
• バッファ: 名称: 50mM Hepes 150mM NaCl / pH: 7.5

要素 #517

名称: Chd1-DBD / タイプ: protein / 記述: chromodomain helicase DNA binding domain / 分子量: 31.096 / 分子数: 1 / 由来: Saccharomyces cerevisiae / 参照: UniProt: P32657
配列:

RRARANDMDS IGESEVRALY KAILKFGNLK EILDELIADG TLPVKSFEKY GETYDEMMEA AKDCVHEEEK NRKEILEKLE KHATAYRAKL KSGEIKAENQ PKDNPLTRLS LKKREKKAVL FNFKGVKSLN AESLLSRVED LKYLKNLINS NYKDDPLKFS LGNNTPKPVQ NWSSNWTKEE DEKLLIGVFK YGYGSWTQIR DDPFLGITDK IFLNEVHNPV AKKSASSSDT TPTPSKKGKG ITGSSKKVPG AIHLGRRVDY LLSFLRGGLN TKSPSA

実験情報

• ビーム: 設備名称: DORIS III X33 / 地域: Hamburg / 国: Germany / 形状: 0.6 / 線源: X-ray synchrotron / 波長: 0.154 Å / スペクトロメータ・検出器間距離: 5 mm
• 検出器: 名称: Pilatus 1M-W / Pixsize x: 0.172 mm

スキャン

タイトル: DNA binding domain of S. cerevisiae Chromo domain-
測定日: 2009年11月20日 / 保管温度: 10 °C / セル温度: 10 °C / 照射時間: 30 sec. / 単位: 1/nm /

	Min	Max
Q	0.1201	6.237

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 1123 /

	Min	Max
Q	0.157483	3.15056
P(R) point	1	1123
R	0	8.39

結果

カーブのタイプ: merged
コメント: The DNA binding module of Saccharomyces cerevisiae Chd1 protein.

	実験値	Standard
分子量	31.663 kDa	31.663 kDa

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	34.48	0.033	34.63	0.039
慣性半径, Rg	2.6 nm	0.003	2.6 nm	0.06

	Min	Max
D	-	8.3
Guinier point	1	143