5J70: The Chd1 DNA-binding domain

The Chd1 DNA-binding domain in complex with 17mer DNA duplex. Determined by X-ray diffraction at 2.96 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 2.96 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
Chains: 6
Atoms: 5,055
Mol. weight: 81.84 kDa
Released: 21 Jun 2017

Explore 5J70 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J70 contains 23 α-helices and 4 β-strands across 2 chains. 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	1013-1025	13
α-helix	1029-1031	3
α-helix	1032-1036	5
α-helix	1046-1091	46
α-helix	1104-1113	10
β-strand	1119-1122	4	1
β-strand	1125-1129	5	1
α-helix	1130-1148	19
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

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1013-1025	13
α-helix	1032-1036	5
α-helix	1046-1091	46
α-helix	1104-1112	9
β-strand	1119-1122	4	2
β-strand	1125-1129	5	2
α-helix	1130-1147	18
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	1250-1264	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromo domain-containing protein 1	A, B	protein	271	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32657 (AlphaFold model)
DNA (5'-d(gpcptpgpgpapapaptptptpcpcpapgpcp*g)-3')	W, Y	DNA	17	synthetic construct
DNA (5'-d(cpgpcptpgpgpapapaptptptpcpcpapgp*c)-3')	X, Z	DNA	17	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5J70_1 Chromo domain-containing protein 1 (chains A, B)
GPDMDSIGESEVRALYKAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDC
VHEEEKNRKEILEKLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFK
GVKSLNAESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKL
LIGVFKYGYGSWTQIRDDPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGS
SKKVPGAIHLGRRVDYLLSFLRGGLNTKSPS

Sequence of entity 2 (W, Y), FASTA

>5J70_2 DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3') (chains W, Y)
GCTGGAAATTTCCAGCG

Sequence of entity 3 (X, Z), FASTA

>5J70_3 DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3') (chains X, Z)
CGCTGGAAATTTCCAGC

Primary citation

Chd1 domains communicate across the DNA gyres of the nucleosome. Nodelman, I.M., Jenkins, K.R., Ren, R. et al. To be published.

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
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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