6XDJ | pdb_00006xdj

Crystal Structure Analysis of MBP-SIN3

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)
D	d6xdjd_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Serratia sp. FS14 ) [TaxId: 1327989 ], (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PAH2 domain-like	8103384	3000467	SCOP2B (2022-06-29)
A	SCOP2 Family	PAH2 domain	8103383	4001017	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PAH2 domain-like	8103384	3000467	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)
D	RNA_pol_Rpb1_5	e6xdjD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: RNA_pol_Rpb1_5	ECOD (v294.1)
C	RNA_pol_Rpb1_5	e6xdjC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: RNA_pol_Rpb1_5	ECOD (v294.1)
B	Acetyltransf_1	e6xdjB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Acetyltransf_1	ECOD (v294.1)
A	Abhydrolase_1	e6xdjA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Abhydrolase_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.1160.11	Mainly Alpha	Up-down Bundle	Paired amphipathic helix 2 (pah2 repeat)	Paired amphipathic helix	CATH (utative)
A	1.20.1160.11	Mainly Alpha	Up-down Bundle	Paired amphipathic helix 2 (pah2 repeat)	Paired amphipathic helix	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02671	Paired amphipathic helix repeat (PAH)	Paired amphipathic helix repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Maltodextrin-binding protein,Transcriptional regulatory protein SIN3	transcription coactivator activity transcription regulator activity transcription coregulator activity transcription corepressor activity identical protein binding protein binding binding	regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process cellular component biogenesis positive regulation of metabolic process cellular component assembly chromatin organization positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process cellular component biogenesis positive regulation of metabolic process cellular component assembly chromatin organization positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation 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 regulation of cellular component organization positive regulation of biological process negative regulation of chromatin organization cellular component organization positive regulation of biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization cellular process negative regulation of heterochromatin organization regulation of rDNA heterochromatin formation rDNA heterochromatin formation nucleolus organization nucleolar chromatin organization negative regulation of rDNA heterochromatin formation nucleus organization organelle organization facultative heterochromatin formation cell division cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus catabolic process macroautophagy autophagy nucleophagy process utilizing autophagic mechanism rDNA chromatin condensation chromosome organization chromosome condensation regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process sexual reproduction reproductive process meiotic cell cycle cell cycle cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition mitotic cell cycle cell cycle process mitotic cell cycle phase transition positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I regulation of transcription by RNA polymerase I double-strand break repair double-strand break repair via nonhomologous end joining DNA damage response DNA repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Rpd3L-Expanded complex Rpd3S complex Rpd3L complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR039774	Transcriptional regulatory protein Sin3-like	Family
A, B, C, D	IPR013194	Histone deacetylase interacting domain	Domain
A, B, C, D	IPR003822	Paired amphipathic helix	Repeat
A, B, C, D	IPR036600	Paired amphipathic helix superfamily	Homologous Superfamily
A, B, C, D	IPR031693	Sin3, C-terminal	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.