3TED: Chd1 DNA-binding domain

Crystal structure of the Chd1 DNA-binding domain in complex with a DNA duplex. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Nov 2011.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 2,512
Mol. weight: 37.83 kDa
Released: 2 Nov 2011

Explore 3TED in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TED contains 12 α-helices and 2 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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1012-1025	14
α-helix	1029-1031	3
α-helix	1032-1037	6
α-helix	1046-1091	46
α-helix	1104-1113	10
β-strand	1119-1122	4	1
β-strand	1125-1129	5	1
α-helix	1130-1150	21
α-helix	1155-1157	3
α-helix	1165-1168	4
α-helix	1177-1190	14
α-helix	1195-1200	6
α-helix	1207-1209	3
α-helix	1250-1265	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromo domain-containing protein 1	A	protein	271	Saccharomyces cerevisiae	P32657 (AlphaFold model)
5'-d(cpcpaptpaptpaptpaptpgpc)-3'	B	DNA	12
5'-d(gpcpaptpaptpaptpaptpgpg)-3'	C	DNA	12

Sequence of entity 1 (A), FASTA

>3TED_1 Chromo domain-containing protein 1 (chains A)
GPDMDSIGESEVRALYKAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDC
VHEEEKNRKEILEKLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFK
GVKSLNAESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKL
LIGVFKYGYGSWTQIRDDPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGS
SKKVPGAIHLGRRVDYLLSFLRGGLNTKSPS

Sequence of entity 2 (B), FASTA

>3TED_2 5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3' (chains B)
CCATATATATGC

Sequence of entity 3 (C), FASTA

>3TED_3 5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*G)-3' (chains C)
GCATATATATGG

Primary citation

DNA-binding domain of Chd1 in complex with a DNA duplex. Sharma, A., Jenkins, K.R., Heroux, A. et al. J Biol Chem (2011).

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
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…
9GD1 4.0 Å, Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of…

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