3TIX | pdb_00003tix

Crystal structure of the Chp1-Tas3 complex core

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	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	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)
B	KOG1911_like	e3tixB2	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: SPOC domain	F: KOG1911_like	ECOD (1.6)
B	EUF08606	e3tixB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: EUF08606	ECOD (1.6)
B	EUF08636	e3tixB3	A: a/b three-layered sandwiches	X: Chromo domain-containing protein 1 (Chp1) domain II (From Topology)	H: Chromo domain-containing protein 1 (Chp1) domain II (From Topology)	T: Chromo domain-containing protein 1 (Chp1) domain II	F: EUF08636	ECOD (1.6)
D	KOG1911_like	e3tixD1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: SPOC domain	F: KOG1911_like	ECOD (1.6)
D	EUF08606	e3tixD3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: EUF08606	ECOD (1.6)
D	EUF08636	e3tixD2	A: a/b three-layered sandwiches	X: Chromo domain-containing protein 1 (Chp1) domain II (From Topology)	H: Chromo domain-containing protein 1 (Chp1) domain II (From Topology)	T: Chromo domain-containing protein 1 (Chp1) domain II	F: EUF08636	ECOD (1.6)
A	EUF08179	e3tixA1	A: alpha bundles	X: Tas3 N-terminal domain (From Topology)	H: Tas3 N-terminal domain (From Topology)	T: Tas3 N-terminal domain	F: EUF08179	ECOD (1.6)
A	Rad60-SLD	e3tixA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
C	EUF08179	e3tixC1	A: alpha bundles	X: Tas3 N-terminal domain (From Topology)	H: Tas3 N-terminal domain (From Topology)	T: Tas3 N-terminal domain	F: EUF08179	ECOD (1.6)
C	Rad60-SLD	e3tixC2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.290.20	Mainly Beta	Beta Barrel	Ku70	Chain: A	CATH (4.3.0)
B	3.40.1010.30	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
B	3.40.50.11490	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	2.40.290.20	Mainly Beta	Beta Barrel	Ku70	Chain: A	CATH (4.3.0)
D	3.40.1010.30	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
D	3.40.50.11490	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	6.10.140.1690	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	6.10.140.1690	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF23340	Chp1 domain II (Chp1_domII)	Chp1 domain II	Chp1 is required for RNA interference-dependent heterochromatin formation in fission yeast, and it is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions, playing a role in stabilizing mic ...	Chp1 is required for RNA interference-dependent heterochromatin formation in fission yeast, and it is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions, playing a role in stabilizing microtubules which allows accurate chromosome segregation [1]. This entry represents the second domain (domain II) of Chp1 which resembles eukaryotic phosphatases and receiver domains of bacterial phosphotransferase signaling systems being part of the Rossmann fold superfamily. This domain makes the interaction surface between Chp1 and Tas3. Chp1 and Tas3 complex solid and versatile platform to recruit both RNAi-dependent and RNAi-independent gene-silencing pathways for locus-specific regulation of heterochromatin [1].	Domain
B, D	PF21484	Chromo domain-containing protein 1-like, PIN domain (Chp1-like_PIN)	Chromo domain-containing protein 1-like, PIN domain	This domain is found at the C-terminal end of Chromo domain- containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in yeast. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silen ...	This domain is found at the C-terminal end of Chromo domain- containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in yeast. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. This entry represents the PIN domain of Chp1, which shows an alpha-beta fold [1].	Domain
B, D	PF22380	Chromo domain-containing protein 1-like, SPOC domain (Chp1-like_SPOC)	Chromo domain-containing protein 1-like, SPOC domain	This entry represents the SPOC domain of Chromo domain-containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in yeast. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silencing ( ...	This entry represents the SPOC domain of Chromo domain-containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in yeast. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation [1].	Domain
A, C	PF22378	Tas3-like, N-terminal domain (Tas3-like_N)	Tas3-like, N-terminal domain	This entry represents the N-terminal domain of Tas3 from Schizosaccharomyces pombe and similar proteins predominantly found in yeast. Tas3 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player ...	This entry represents the N-terminal domain of Tas3 from Schizosaccharomyces pombe and similar proteins predominantly found in yeast. Tas3 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation [1].	Domain
A, C	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Chromo domain-containing protein 1	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding chromatin binding RNA binding nucleic acid binding single-stranded RNA binding DNA binding	cellular process cell cycle chromosome segregation cell cycle process regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process cellular process cell cycle chromosome segregation cell cycle process regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly 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 heterochromatin organization 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 macromolecule metabolic process regulation of metabolic process pericentric heterochromatin organization pericentric heterochromatin formation siRNA-mediated heterochromatin formation siRNA-mediated pericentric heterochromatin formation regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation subtelomeric 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 microtubule organizing center cytoskeleton spindle pole body microtubule cytoskeleton membrane-bounded organelle RITS complex protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membrane-bounded organelle RNAi effector complex intracellular organelle lumen organelle lumen ribonucleoprotein complex nuclear lumen condensed chromosome, centromeric region condensed chromosome
A, C	Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3	regulatory RNA binding RNA binding siRNA binding binding nucleic acid binding molecular adaptor activity protein tag activity molecular tag activity protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis siRNA-mediated heterochromatin formation cellular component assembly chromatin organization pericentric heterochromatin 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 regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis siRNA-mediated heterochromatin formation cellular component assembly chromatin organization pericentric heterochromatin 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 siRNA-mediated pericentric heterochromatin formation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression pericentric heterochromatin formation negative regulation of gene expression constitutive heterochromatin formation regulatory ncRNA-mediated 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 subtelomeric heterochromatin formation cell cycle chromosome segregation cell cycle process silent mating-type cassette heterochromatin formation peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure chromosome, subtelomeric region intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, telomeric region subtelomeric heterochromatin microtubule organizing center intracellular anatomical structure chromosome, subtelomeric region intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, telomeric region subtelomeric heterochromatin microtubule organizing center cytoskeleton spindle pole body microtubule cytoskeleton membrane-bounded organelle RITS complex protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membrane-bounded organelle RNAi effector complex intracellular organelle lumen organelle lumen ribonucleoprotein complex nuclear lumen mating-type region heterochromatin pericentric heterochromatin chromosome, centromeric region cell cortex septin ring cell periphery septin cytoskeleton cytoplasm condensed nuclear chromosome condensed chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR048709	Chop1, PIN domain	Domain
B, D	IPR023780	Chromo domain	Domain
B, D	IPR049938	Chp1, SPOC domain	Domain
B, D	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
B, D	IPR023779	Chromo domain, conserved site	Conserved Site
B, D	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family
B, D	IPR000953	Chromo/chromo shadow domain	Domain
B, D	IPR056341	Chp1, domain II	Domain
B, D	IPR049937	Chp1, chromodomain	Domain
B, D	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A, C	IPR049112	Tas3, C-terminal helical domain	Domain
A, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C	IPR000626	Ubiquitin-like domain	Domain
A, C	IPR022617	Rad60/SUMO-like 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.