3MWY | pdb_00003mwy

Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth W]	SCOP2B Superfamily	Chromo domain-like	8039987	3000161	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth W]	Chromo	e3mwyW1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
A [auth W]	SNF2_N	e3mwyW3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SNF2_N	ECOD (1.6)
A [auth W]	Helicase_C	e3mwyW4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth W]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A [auth W]	3.40.50.10810	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tandem AAA-ATPase domain	CATH (4.3.0)
A [auth W]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth W]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A [auth W]	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain		Domain
A [auth W]	PF00176	SNF2-related domain (SNF2-rel_dom)	SNF2-related domain	This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as w ...	This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1)[1,2,3]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth W]	Chromo domain-containing protein 1	protein binding binding histone binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding protein binding binding histone binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity ATP-dependent chromatin remodeler activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding rDNA binding nucleosome array spacer activity histone octamer slider activity chromatin DNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair regulation of cellular process RNA metabolic process regulation of transcriptional start site selection at RNA polymerase II promoter regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process DNA-templated transcriptional start site selection transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription, start site selection transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation regulation of gene expression biosynthetic process regulation of transcription initiation by RNA polymerase II regulation of macromolecule biosynthetic process transcriptional start site selection at RNA polymerase II promoter regulation of DNA-templated transcription regulation of metabolic process DNA-templated transcription termination termination of RNA polymerase II transcription cellular component organization organelle organization chromosome organization sister chromatid cohesion cellular component organization or biogenesis cell cycle cell cycle process regulation of chromatin organization regulation of cellular component organization chromatin organization transcription by RNA polymerase I termination of RNA polymerase I transcription DNA recombination recombinational repair double-strand break repair via homologous recombination transcription elongation by RNA polymerase II DNA-templated transcription elongation negative regulation of biological process negative regulation of DNA-templated DNA replication negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process DNA-templated DNA replication negative regulation of DNA replication negative regulation of metabolic process DNA replication regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication protein-DNA complex organization protein-containing complex organization chromatin remodeling nucleosome organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SLIK (SAGA-like) complex intracellular protein-containing complex nucleolar chromatin nucleus membrane-enclosed lumen nuclear chromosome nucleolus intracellular organelle lumen organelle lumen nuclear lumen peptidase complex SAGA complex site of double-strand break site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth W]	IPR023780	Chromo domain	Domain
A [auth W]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A [auth W]	IPR023779	Chromo domain, conserved site	Conserved Site
A [auth W]	IPR041150	Chromodomain helicase DNA-binding domain	Domain
A [auth W]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A [auth W]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A [auth W]	IPR000330	SNF2, N-terminal domain	Domain
A [auth W]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth W]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A [auth W]	IPR000953	Chromo/chromo shadow domain	Domain
A [auth W]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth W]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth W]	IPR056302	ATP-dependent helicase CHD1-2/hrp3, HTH domain	Domain
A [auth W]	IPR025260	Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.