2DY8: Second chromodomain of yeast Chd1

Solution structure of the second chromodomain of yeast Chd1. Determined by solution NMR. Released 28 Nov 2006.

Method: Solution NMR
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 586
Mol. weight: 8.29 kDa
Released: 28 Nov 2006

Explore 2DY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2DY8 contains 2 α-helices and 3 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	287-297	11	1
β-strand	303-311	9	1
β-strand	320-323	4	1
α-helix	324-330	7
α-helix	332-341	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromo domain protein 1	A	protein	69	Saccharomyces cerevisiae	P32657 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2DY8_1 Chromo domain protein 1 (chains A)
DEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHF
QNRENSKIL

Primary citation

Structural Polymorphism of Chromodomains in Chd1. Okuda, M., Horikoshi, M., Nishimura, Y. J Mol Biol (2007) 365:1047-1062. DOI 10.1016/j.jmb.2006.10.039 · PubMed

Other PDB entries of the same protein (UniProt P32657 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XB0 2.0 Å, DNA-binding domain from Saccharomyces cerevisiae chromatin- remodelling protein Chd1
3TED 2.0 Å, Crystal structure of the Chd1 DNA-binding domain in complex with a DNA duplex
2H1E 2.2 Å, Tandem chromodomains of budding yeast CHD1
7TN2 2.3 Å, Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from…
9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
7NKX 2.9 Å, RNA polymerase II-Spt4/5-nucleosome-Chd1 structure
9N6K 2.9 Å, 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain
5J70 2.96 Å, The Chd1 DNA-binding domain in complex with 17mer DNA duplex
9GD3 3.0 Å, Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA.
3MWY 3.7 Å, Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler
9R5S 3.8 Å, Structural characterisation of chromatin remodelling intermediates supports linker DNA…

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