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Yorodumi- SASDBV7: Chromo-ATPase-DBD domains of chromo domain-containing protein 1 (... -
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-Basic information
Entry | Database: SASBDB / ID: SASDBV7 |
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Sample | Chromo-ATPase-DBD domains of chromo domain-containing protein 1 (Chd1: 133-1305)
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Function / homology | Function and homology information 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 / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / SAGA complex ...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 / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / 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 / 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 Similarity search - Function |
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 ...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 ...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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-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) |
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-Sample
Sample | Name: Chromo-ATPase-DBD domains of chromo domain-containing protein 1 (Chd1: 133-1305) Specimen concentration: 0.20-3.50 |
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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 ...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 synchrotronSynchrotron / Wavelength: 0.154 Å / Dist. spec. to detc.: 5 mm | |||||||||||||||||||||||||||||||||
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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 /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 707 /
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Result | Type of curve: extrapolated Comments: The chromo-helicase-DNA binding domains of Saccharomyces cerevisiae Chd1.
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