SASDBW7: N-terminal and chromo-ATPase-DBD domains of chromo domain-contain...

Basic information

• Entry: Database: SASBDB / ID: SASDBW7

Sample

N-terminal and chromo-ATPase-DBD domains of chromo domain-containing protein 1 (Chd1: 1-1305)

• chromodomain helicase DNA binding domain (protein), Chd1, 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 / nucleosome organization / rDNA binding / SLIK (SAGA-like) complex / SAGA complex / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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

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 / 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

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 #917: ; Type: dummy / Software: GASBOR (2.3i) / Radius of dummy atoms: 1.90 A / Symmetry: C1 / Chi-square value: 1.90 / P-value: 0.000020; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: N-terminal and chromo-ATPase-DBD domains of chromo domain-containing protein 1 (Chd1: 1-1305); Specimen concentration: 0.50-4.00
• Buffer: Name: 50mM Hepes 150mM NaCl / pH: 7.5

Entity #519

Name: Chd1 / Type: protein / Description: chromodomain helicase DNA binding domain / Formula weight: 150.014 / Num. of mol.: 1 / Source: Saccharomyces cerevisiae / References: UniProt: P32657
Sequence:

MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE DEFEDEEGEE DSGEDEDEED FEEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST VKIPTRFSNR QNKTVNYNID YSDDDLLESE DDYGSEEALS EENVHEASAN PQPEDFHGID IVINHRLKTS LEEGKVLEKT VPDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK RLDNYCKQFI IEDQQVRLDP YVTAEDIEIM DMERERRLDE FEEFHVPERI IDSQRASLED GTSQLQYLVK WRRLNYDEAT WENATDIVKL APEQVKHFQN RENSKILPQY SSNYTSQRPR FEKLSVQPPF IKGGELRDFQ LTGINWMAFL WSKGDNGILA DEMGLGKTVQ TVAFISWLIF ARRQNGPHII VVPLSTMPAW LDTFEKWAPD LNCICYMGNQ KSRDTIREYE FYTNPRAKGK KTMKFNVLLT TYEYILKDRA ELGSIKWQFM AVDEAHRLKN AESSLYESLN SFKVANRMLI TGTPLQNNIK ELAALVNFLM PGRFTIDQEI DFENQDEEQE EYIHDLHRRI QPFILRRLKK DVEKSLPSKT ERILRVELSD VQTEYYKNIL TKNYSALTAG AKGGHFSLLN IMNELKKASN HPYLFDNAEE RVLQKFGDGK MTRENVLRGL IMSSGKMVLL DQLLTRLKKD GHRVLIFSQM VRMLDILGDY LSIKGINFQR LDGTVPSAQR RISIDHFNSP DSNDFVFLLS TRAGGLGINL MTADTVVIFD SDWNPQADLQ AMARAHRIGQ KNHVMVYRLV SKDTVEEEVL ERARKKMILE YAIISLGVTD GNKYTKKNEP NAGELSAILK FGAGNMFTAT DNQKKLEDLN LDDVLNHAED HVTTPDLGES HLGGEEFLKQ FEVTDYKADI DWDDIIPEEE LKKLQDEEQK RKDEEYVKEQ LEMMNRRDNA LKKIKNSVNG DGTAANSDSD DDSTSRSSRR RARANDMDSI GESEVRALYK AILKFGNLKE ILDELIADGT LPVKSFEKYG ETYDEMMEAA KDCVHEEEKN RKEILEKLEK HATAYRAKLK SGEIKAENQP KDNPLTRLSL KKREKKAVLF NFKGVKSLNA ESLLSRVEDL KYLKNLINSN YKDDPLKFSL GNNTPKPVQN WSSNWTKEED EKLLIGVFKY GYGSWTQIRD DPFLGITDKI FLNEVHNPVA KKSASSSDTT PTPSKKGKGI TGSSKKVPGA IHLGRRVDYL LSFLRGGLNT KSPSADIGSK KLPTGPSKKR QRKPANHSKS MTPEI

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.154 Å / Dist. spec. to detc.: 5 mm
• Detector: Name: Pilatus 2M

Scan

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

	Min	Max
Q	0.1513	4.945

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 716 /

	Min	Max
Q	0.1306	1.778
P(R) point	1	716
R	0	16

Result

Type of curve: extrapolated / Comments: Saccharomyces cerevisiae Chd1 protein. /

	Experimental	Porod
MW	150 kDa	170 kDa
Volume	-	340 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	1.53	0.003	1.56	0.0072
Radius of gyration, Rg	4.85 nm	0.01	4.9 nm	0.03

	Min	Max
D	-	16
Guinier point	3	51