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Yorodumi- SASDBU7: DNA binding domain (DBD) of chromo domain-containing protein 1 (C... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDBU7 |
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Sample | DNA binding domain (DBD) of chromo domain-containing protein 1 (Chd1: 1009-1274)
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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 / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion ...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 / SAGA complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / 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 / double-strand break repair via homologous recombination / chromatin DNA binding / site of double-strand break / 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 #919 | Type: dummy / Software: GASBOR (2.3i) / Radius of dummy atoms: 1.90 A / Symmetry: C1 / Chi-square value: 2.10 Search similar-shape structures of this assembly by Omokage search (details) |
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-Sample
Sample | Name: DNA binding domain (DBD) of chromo domain-containing protein 1 (Chd1: 1009-1274) Specimen concentration: 1.20-9.90 |
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Buffer | Name: 50mM Hepes 150mM NaCl / pH: 7.5 |
Entity #517 | Name: Chd1-DBD / Type: protein / Description: chromodomain helicase DNA binding domain / Formula weight: 31.096 / Num. of mol.: 1 / Source: Saccharomyces cerevisiae / References: UniProt: P32657 Sequence: RRARANDMDS IGESEVRALY KAILKFGNLK EILDELIADG TLPVKSFEKY GETYDEMMEA AKDCVHEEEK NRKEILEKLE KHATAYRAKL KSGEIKAENQ PKDNPLTRLS LKKREKKAVL FNFKGVKSLN AESLLSRVED LKYLKNLINS NYKDDPLKFS LGNNTPKPVQ ...Sequence: 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 |
-Experimental information
Beam | Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotron / Wavelength: 0.154 Å / Dist. spec. to detc.: 5 mm | ||||||||||||||||||||||||||||||
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Detector | Name: Pilatus 1M-W / Pixsize x: 0.172 mm | ||||||||||||||||||||||||||||||
Scan | Title: DNA binding domain of S. cerevisiae Chromo domain- / Measurement date: Nov 20, 2009 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 30 sec. / Unit: 1/nm /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 1123 /
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Result | Type of curve: merged Comments: The DNA binding module of Saccharomyces cerevisiae Chd1 protein.
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