4O9I | pdb_00004o9i

Structure of CHD4 double chromodomains depicts cooperative folding for DNA binding

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth X]	SCOP2B Superfamily	Chromo domain-like	8072503	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 X]	BON	e4o9iX1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: Ribosomal protein S7	T: Ribosomal protein S7	F: BON	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth X]	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X]	Chromodomain-helicase-DNA-binding protein 4	protein binding binding histone binding histone deacetylase binding enzyme binding transcription factor binding transcription coregulator binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding protein binding binding histone binding histone deacetylase binding enzyme binding transcription factor binding transcription coregulator binding 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 DNA binding nucleic acid binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity transcription corepressor activity transcription regulator activity transcription coregulator activity 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 cation binding transition metal ion binding zinc ion binding metal ion binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process multicellular organismal process regulation of cellular component organization cellular component organization developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process multicellular organismal process regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development regulation of synapse structure or activity regulation of synapse assembly synapse organization cellular component organization or biogenesis regulation of biological quality system development nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process presynapse organization terminal button organization regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment cellular response to stimulus double-strand break repair response to stimulus DNA recombination DNA metabolic process cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of gene expression chromatin organization chromatin remodeling	cellular anatomical structure membrane neuron to neuron synapse synapse cell junction asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse intracellular anatomical structure cytoplasm intracellular organelle organelle cellular anatomical structure membrane neuron to neuron synapse synapse cell junction asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular organelle lumen histone deacetylase complex nucleoplasm NuRD complex SWI/SNF superfamily-type complex catalytic complex intracellular membrane-bounded organelle organelle lumen CHD-type complex nuclear lumen chromosome, telomeric region chromosomal region RNA polymerase II transcription regulator complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X]	IPR001965	Zinc finger, PHD-type	Domain
A [auth X]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A [auth X]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth X]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth X]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth X]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth X]	IPR012958	CHD, N-terminal	Domain
A [auth X]	IPR012957	CHD, C-terminal 2	Domain
A [auth X]	IPR023780	Chromo domain	Domain
A [auth X]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A [auth X]	IPR019787	Zinc finger, PHD-finger	Domain
A [auth X]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A [auth X]	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
A [auth X]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A [auth X]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A [auth X]	IPR000330	SNF2, N-terminal domain	Domain
A [auth X]	IPR000953	Chromo/chromo shadow domain	Domain
A [auth X]	IPR009462	CHD subfamily II, SANT-like domain	Domain
A [auth X]	IPR009463	Domain of unknown function DUF1087	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X]	Pharos: Q14839	Sifrim-Hitz-Weiss syndrome endometrial carcinoma intellectual disability schizophrenia astrocytic tumor endometrial cancer glioblastoma lung adenocarcinoma osteosarcoma psoriasis autism malignant mesothelioma ovarian cancer rheumatoid arthritis developmental disability Sifrim-Hitz-Weiss syndrome endometrial carcinoma intellectual disability schizophrenia astrocytic tumor endometrial cancer glioblastoma lung adenocarcinoma osteosarcoma psoriasis autism malignant mesothelioma ovarian cancer rheumatoid arthritis developmental disability Endometrial Neoplasms large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor

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.