6FTO

Crystal structure of the Chp2 chromoshadow domain in complex with N-terminal domain of chromatin remodeler Mit1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6ftoa_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
B	d6ftob_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Chromo domain-like	8095625	3000161	SCOP2B (2022-06-29)
B	SCOP2 Family	Chromo domain	8095624	4000375	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Chromo domain-like	8095625	3000161	SCOP2 (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	PF01393	e6ftoA1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF01393	ECOD (1.6)
B	PF01393	e6ftoB1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF01393	ECOD (1.6)
C	F_UNCLASSIFIED	e6ftoC1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01393	Chromo shadow domain (Chromo_shadow)	Chromo shadow domain	This domain is distantly related to Pfam:PF00385. This domain is always found in association with a chromo domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Chromo domain-containing protein 2	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding histone binding protein-containing complex binding chromatin binding methylated histone binding modification-dependent protein binding methylation-dependent protein binding	subtelomeric heterochromatin formation regulation of cellular process cellular biosynthetic process negative regulation of biological process telomere organization negative regulation of cellular metabolic process cellular component organization protein-DNA complex organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis subtelomeric heterochromatin formation regulation of cellular process cellular biosynthetic process negative regulation of biological process telomere organization negative regulation of cellular metabolic process cellular component organization protein-DNA complex organization organic substance metabolic process chromatin organization organic substance biosynthetic process 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 protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation chromosome organization regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organelle organization negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process silent mating-type cassette heterochromatin formation pericentric heterochromatin formation regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation nucleolar chromatin organization rDNA heterochromatin formation nucleus organization nucleolus organization facultative heterochromatin formation	protein-containing complex intracellular anatomical structure protein-DNA complex mating-type region heterochromatin chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome, subtelomeric region chromosome, telomeric region protein-containing complex intracellular anatomical structure protein-DNA complex mating-type region heterochromatin chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome, subtelomeric region chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle pericentric heterochromatin chromosome, centromeric region
C	Chromatin remodeling factor mit1	catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein binding binding histone binding protein-containing complex binding chromatin binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA adenyl ribonucleotide binding nucleotide binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein binding binding histone binding protein-containing complex 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 organic cyclic compound 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 nucleosome binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process 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 protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression 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 nucleosome organization	protein-containing complex intracellular anatomical structure protein-DNA complex heterochromatin island chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle mating-type region heterochromatin chromosome, subtelomeric region protein-containing complex intracellular anatomical structure protein-DNA complex heterochromatin island chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle mating-type region heterochromatin chromosome, subtelomeric region chromosome, telomeric region chromosomal region pericentric heterochromatin chromosome, centromeric region rDNA heterochromatin membrane-bounded organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000953	Chromo/chromo shadow domain	Domain
A, B	IPR023780	Chromo domain	Domain
A, B	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B	IPR008251	Chromo shadow domain	Domain
C	IPR000330	SNF2, N-terminal	Domain
C	IPR001965	Zinc finger, PHD-type	Domain
C	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
C	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
C	IPR019787	Zinc finger, PHD-finger	Domain
C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
C	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
C	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR041299	Chromatin remodeling factor Mit1, C-terminal Zn finger 1	Domain
C	IPR001650	Helicase, C-terminal domain-like	Domain
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C	IPR040934	Mit1, C-terminal Zn finger 2	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 R01GM133198.