5IKF | pdb_00005ikf

Crystal structure of the C-terminal domain of the Mit1 nucleosome remodeler in complex with Clr1

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	EUF08732	e5ikfA1	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Chromatin remodeling factor Mit1 C-terminal Zn fingers (From Topology)	T: Chromatin remodeling factor Mit1 C-terminal Zn fingers	F: EUF08732	ECOD (1.6)
A	EUF08733	e5ikfA2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Chromatin remodeling factor Mit1 C-terminal Zn fingers (From Topology)	T: Chromatin remodeling factor Mit1 C-terminal Zn fingers	F: EUF08733	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18586	Chromatin remodeling factor Mit1 C-terminal Zn finger 1 (zf-CCCH_7)	Chromatin remodeling factor Mit1 C-terminal Zn finger 1	The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin re ...	The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins. The Mit1 C terminus contains two zinc binding motifs (CCHC zinc fingers) at the C-terminus onto which the alpha helices from both Clr1 and Mit1 pack. The Mit1 chromatin remodeler uses its C-terminal domain to intimately bind to the N-terminal half of Clr1 to integrate into the SHREC complex. This is entry represents the first C-terminal zinc-binding domain found on Mit-1 [1].	Domain
A	PF18585	Chromatin remodeling factor Mit1 C-terminal Zn finger 2 (zf-CCCH_6)	Chromatin remodeling factor Mit1 C-terminal Zn finger 2	The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin re ...	The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins. The Mit1 C terminus contains two zinc binding motifs (CCHC zinc fingers) at the C-terminus onto which the alpha helices from both Clr1 and Mit1 pack. The Mit1 chromatin remodeler uses its C-terminal domain to intimately bind to the N-terminal half of Clr1 to integrate into the SHREC complex. This is entry represents the second C-terminal zinc-binding domain found on Mit-1 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Chromatin remodeling factor mit1	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein binding binding histone binding chromatin binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein binding binding histone binding chromatin binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA 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 nucleosome array spacer activity histone octamer slider 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 metal ion binding protein-containing complex binding nucleosome binding	regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process pericentric heterochromatin formation subtelomeric heterochromatin formation protein-DNA complex organization protein-containing complex organization nucleosome organization nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle heterochromatin island chromatin chromosome heterochromatin chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle heterochromatin island chromatin chromosome heterochromatin chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin pericentric heterochromatin chromosome, centromeric region rDNA heterochromatin membrane-bounded organelle protein-containing complex ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex SHREC 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
B	Cryptic loci regulator protein 1	cation binding ion binding binding metal ion binding small molecule binding	subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process silent mating-type cassette heterochromatin formation pericentric heterochromatin formation nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation	intracellular organelle rDNA heterochromatin cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin mating-type region heterochromatin membrane-bounded organelle protein-containing complex ATPase complex intracellular organelle rDNA heterochromatin cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin mating-type region heterochromatin membrane-bounded organelle protein-containing complex ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex SHREC 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, subtelomeric region chromosome, telomeric region chromosomal region pericentric heterochromatin chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000330	SNF2, N-terminal	Domain
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR041299	Chromatin remodeling factor Mit1, C-terminal Zn finger 1	Domain
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR040934	Mit1, C-terminal Zn finger 2	Domain
B	IPR013087	Zinc finger C2H2-type	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.