3MWY: Chromo domain-containing protein 1

Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler. Determined by X-ray diffraction at 3.7 Å resolution. Released 29 Sept 2010.

Method: X-ray diffraction
Resolution: 3.7 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 5,743
Mol. weight: 92.97 kDa
Ligands: AGS
Released: 29 Sept 2010

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

Secondary structure: helices and β-sheets

3MWY contains 39 α-helices and 28 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 W: 39 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	178	1	1
β-strand	181-186	6	2
α-helix	204-210	7
β-strand	212-216	5	2
α-helix	217	1
β-strand	226-228	3	2
α-helix	230-233	4
β-strand	237	1	1
α-helix	240-246	7
α-helix	247-251	5
α-helix	252-256	5
α-helix	264-281	18
β-strand	287-290	4	3
α-helix	295	1
β-strand	296-297	2	4
β-strand	303-304	2	4
β-strand	306	1	5
β-strand	309-311	3	3
β-strand	320	1	3
β-strand	323	1	5
α-helix	324-327	4
α-helix	332-340	9
α-helix	379-391	13
β-strand	397-399	3	6
α-helix	401-402	2
α-helix	409-422	14
β-strand	428-431	4	7
α-helix	437-447	11
β-strand	453-455	3	7
α-helix	461-470	10
β-strand	487-490	4	7
α-helix	494-497	4
α-helix	499-503	5
β-strand	506-512	7	7
α-helix	515-518	4
α-helix	524-529	6
β-strand	533-537	5	7
β-strand	538-540	3	6
α-helix	550-559	10
α-helix	578-588	11
α-helix	591-593	3
β-strand	594-596	3	6
α-helix	599-602	4
β-strand	609-616	8	8
α-helix	617-619	3
α-helix	620-632	13
α-helix	648-660	13
α-helix	662-664	3
α-helix	668-672	5
α-helix	684-692	9
α-helix	695-707	13
β-strand	714-718	5	8
α-helix	721-734	14
β-strand	739-741	3	8
α-helix	747-755	9
β-strand	767-770	4	8
α-helix	771-774	4
β-strand	785-788	4	8
α-helix	796-802	7
β-strand	814-821	8	8
α-helix	825-836	12
α-helix	862-869	8
α-helix	880-887	8
α-helix	891-897	7
β-strand	899-900	2	8
β-strand	911-912	2	6
α-helix	915-919	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromo domain-containing protein 1	W	protein	800	Saccharomyces cerevisiae	P32657 (AlphaFold model)

Sequence of entity 1 (W), FASTA

>3MWY_1 Chromo domain-containing protein 1 (chains W)
GPSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGIDIVINHRLKTSLEEGKVLEK
TVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFIIEDQQVRLD
PYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEA
TWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDF
QLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPA
WLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDR
AELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFL
MPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVELS
DVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDG
KMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQ
RLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADL
QAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEYAIISLGVTDGNKYTKKNE
PNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAEDHVTTPDLGESHLGGEEFLK
QFEVTDYKADIDWDDIIPEE

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	1

Primary citation

The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Hauk, G., McKnight, J.N., Nodelman, I.M. et al. Mol Cell (2010) 39:711-723. DOI 10.1016/j.molcel.2010.08.012 · 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.
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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