SASDBV7: Chromo-ATPase-DBD domains of chromo domain-containing protein 1 (...

Basic information

• Entry: Database: SASBDB / ID: SASDBV7

Sample

Chromo-ATPase-DBD domains of chromo domain-containing protein 1 (Chd1: 133-1305)

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

Function / homology

Function:

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 / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / : / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus

Domain/homology:

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 / ATP-dependent helicase CHD1-2/hrp3 HTH domain / 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 / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / 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

Component:

Chromo domain-containing protein 1

• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Citation: Journal: Elife / Year: 2017; Title: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.; Authors: 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 / ; Abstract: 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.

Contact author

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

Models

• Model #918: ; Type: dummy / Software: GASBOR (2.3i) / Radius of dummy atoms: 1.90 A / Symmetry: C1 / Chi-square value: 2.21; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Chromo-ATPase-DBD domains of chromo domain-containing protein 1 (Chd1: 133-1305); Specimen concentration: 0.20-3.50
• Buffer: Name: 50mM Hepes 150mM NaCl / pH: 7.5

Entity #518

Name: Chd1-CH / Type: protein / Description: chromodomain helicase DNA binding domain / Formula weight: 134.574 / Num. of mol.: 1 / Source: Saccharomyces cerevisiae / References: UniProt: P32657
Sequence:

KTVNYNIDYS DDDLLESEDD YGSEEALSEE NVHEASANPQ PEDFHGIDIV INHRLKTSLE EGKVLEKTVP DLNNCKENYE FLIKWTDESH LHNTWETYES IGQVRGLKRL DNYCKQFIIE DQQVRLDPYV TAEDIEIMDM ERERRLDEFE EFHVPERIID SQRASLEDGT SQLQYLVKWR RLNYDEATWE NATDIVKLAP EQVKHFQNRE NSKILPQYSS NYTSQRPRFE KLSVQPPFIK GGELRDFQLT GINWMAFLWS KGDNGILADE MGLGKTVQTV AFISWLIFAR RQNGPHIIVV PLSTMPAWLD TFEKWAPDLN CICYMGNQKS RDTIREYEFY TNPRAKGKKT MKFNVLLTTY EYILKDRAEL GSIKWQFMAV DEAHRLKNAE SSLYESLNSF KVANRMLITG TPLQNNIKEL AALVNFLMPG RFTIDQEIDF ENQDEEQEEY IHDLHRRIQP FILRRLKKDV EKSLPSKTER ILRVELSDVQ TEYYKNILTK NYSALTAGAK GGHFSLLNIM NELKKASNHP YLFDNAEERV LQKFGDGKMT RENVLRGLIM SSGKMVLLDQ LLTRLKKDGH RVLIFSQMVR MLDILGDYLS IKGINFQRLD GTVPSAQRRI SIDHFNSPDS NDFVFLLSTR AGGLGINLMT ADTVVIFDSD WNPQADLQAM ARAHRIGQKN HVMVYRLVSK DTVEEEVLER ARKKMILEYA IISLGVTDGN KYTKKNEPNA GELSAILKFG AGNMFTATDN QKKLEDLNLD DVLNHAEDHV TTPDLGESHL GGEEFLKQFE VTDYKADIDW DDIIPEEELK KLQDEEQKRK DEEYVKEQLE MMNRRDNALK KIKNSVNGDG TAANSDSDDD STSRSSRRRA RANDMDSIGE SEVRALYKAI LKFGNLKEIL DELIADGTLP VKSFEKYGET YDEMMEAAKD CVHEEEKNRK EILEKLEKHA TAYRAKLKSG EIKAENQPKD NPLTRLSLKK REKKAVLFNF KGVKSLNAES LLSRVEDLKY LKNLINSNYK DDPLKFSLGN NTPKPVQNWS SNWTKEEDEK LLIGVFKYGY GSWTQIRDDP FLGITDKIFL NEVHNPVAKK SASSSDTTPT PSKKGKGITG SSKKVPGAIH LGRRVDYLLS FLRGGLNTKS PSADIGSKKL PTGPSKKRQR KPANHSKSMT PEI

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.154 Å / Dist. spec. to detc.: 5 mm
• Detector: Name: Pilatus 2M

Scan

Title: Chromodomain-ATPase-DBD domains of S. cerevisiae C / Measurement date: Nov 30, 2008 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 120 sec. / Unit: 1/nm /

	Min	Max
Q	0.1375	4.945

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 707 /

	Min	Max
Q	0.1697	1.796
P(R) point	1	707
R	0	15.45

Result

Type of curve: extrapolated
Comments: The chromo-helicase-DNA binding domains of Saccharomyces cerevisiae Chd1.

	Experimental	Porod
MW	138 kDa	140 kDa
Volume	-	280 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.915	0.003	0.92	0.0044
Radius of gyration, Rg	4.2 nm	0.02	4.18 nm	0.02

	Min	Max
D	-	15.4
Guinier point	15	76