4B4C | pdb_00004b4c

Crystal structure of the DNA-binding domain of human CHD1.

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	KOG0384	e4b4cA6	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KOG0384	ECOD (1.6)
A	SLIDE_1	e4b4cA5	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: SLIDE_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF23588	ATP-dependent helicase CHD1-2/hrp3 HTH domain (HTH_CHD1_Hrp3)	ATP-dependent helicase CHD1-2/hrp3 HTH domain	This domain is found in ATP-dependent helicase CHD1/2 from animals and its orthologues hrp1/3 (Hrp1/3) from Schizosaccharomyces pombe. CHD1 is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the tran ...	This domain is found in ATP-dependent helicase CHD1/2 from animals and its orthologues hrp1/3 (Hrp1/3) from Schizosaccharomyces pombe. CHD1 is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and it is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step [1-3]. Hrp1/3 are involved in heterochromatin silencing [4,5]. This domain is predicted to adopt an HTH structure and is often found C-terminal to Pfam:PF18196.	Domain
A	PF18375	CDH1/2 SANT-Helical linker 1 (CDH1_2_SANT_HL1)	CDH1/2 SANT-Helical linker 1	CDH1 is an ATP-dependent chromatin-remodelling factor and plays an important role in regulating nucleosome assembly and mobilization. CHD1 consists of double chromodomain, SNF2-related ATPase domain, and a C-terminal DNA-binding domain. The DNA-bindi ...	CDH1 is an ATP-dependent chromatin-remodelling factor and plays an important role in regulating nucleosome assembly and mobilization. CHD1 consists of double chromodomain, SNF2-related ATPase domain, and a C-terminal DNA-binding domain. The DNA-binding domain contains SANT (Swi3, Ada2, N-CoR, TFIIIB) and SLIDE (SANT-like ISWI) domains in its C-terminal region [1]. SANT domains are structurally related to Myb-like domains are common motifs found in chromatin interacting proteins. Deletion of individual SANT or SLIDE domains in CDH1 does not significantly affect nucleosome binding, but combined deletion of both domains severely compromise binding, suggesting that the SANT-SLIDE motif recognizes DNA/nucleosomes as a single cooperative unit. SANT sequences of Chd1 proteins are the most distantly relation group of sequences relation to other SANT/Myb sequences, and are more diverse than other SANT proteins [2]. The SANT and SLIDE regions are well conserved in both Chd1 and ISWI (imitation switch) remodelling enzymes [3]. This domain comprises the SANT region and the helical linker region 1 (HL1).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CHROMODOMAIN-HELICASE-DNA-BINDING 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 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 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 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 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 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	host-mediated activation of viral transcription biological process involved in interspecies interaction between organisms host-mediated perturbation of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated activation of viral process host-mediated perturbation of symbiont process cellular component organization protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling cellular process cellular component organization or biogenesis host-mediated activation of viral transcription biological process involved in interspecies interaction between organisms host-mediated perturbation of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated activation of viral process host-mediated perturbation of symbiont process cellular component organization protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling cellular process cellular component organization or biogenesis nucleosome organization	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome nuclear chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023780	Chromo domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR023779	Chromo domain, conserved site	Conserved Site
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR000330	SNF2, N-terminal domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR056302	ATP-dependent helicase CHD1-2/hrp3, HTH domain	Domain
A	IPR025260	Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain	Domain
A	IPR040793	CDH1/2, SANT-Helical linker 1	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O14646	prostate cancer Pilarowski-Bjornsson syndrome colorectal cancer adrenal cortex carcinoma Crohn disease interstitial lung disease malignant glioma ovarian cancer colorectal adenoma diabetes mellitus large cell medulloblastoma malignant mesothelioma Prostatic Neoplasms glioblastoma lung cancer prostate cancer Pilarowski-Bjornsson syndrome colorectal cancer adrenal cortex carcinoma Crohn disease interstitial lung disease malignant glioma ovarian cancer colorectal adenoma diabetes mellitus large cell medulloblastoma malignant mesothelioma Prostatic Neoplasms glioblastoma lung cancer medulloblastoma primitive neuroectodermal tumor ulcerative colitis

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.