4BY6 | pdb_00004by6

Yeast Not1-Not2-Not5 complex

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)
C	SCOP2 Family	NOT2_3_5 domain-like	8045466	4004482	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	NOT2_3_5 domain-like	8090761	3002454	SCOP2 (2022-06-29)
E	SCOP2 Family	NOT2_3_5 domain-like	8045467	4004482	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	NOT2_3_5 domain-like	8090762	3002454	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	NOT2_3_5 domain-like	8090762	3002454	SCOP2B (2022-06-29)
D	SCOP2 Family	Not1-like	8045229	4004363	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	ARM repeat-like	8057079	3000116	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	ARM repeat-like	8057080	3000116	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8057079	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8057080	3000116	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)
F	HABP4_PAI-RBP1	e4by6F1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)
C	Evr1_Alr	e4by6C1	A: a/b three-layered sandwiches	X: HTH	H: SH3	T: SH3	F: Evr1_Alr	ECOD (v294.1)
E	NOT2_3_5_C	e4by6E1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: NOT2_3_5_C	ECOD (v294.1)
B	RNA_pol_I_A49	e4by6B1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RNA_pol_I_A49	ECOD (v294.1)
D	RNA_pol_I_A49	e4by6D1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RNA_pol_I_A49	ECOD (v294.1)
A	Not1	e4by6A1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Not1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.30.30.1020	Mainly Beta	Roll	SH3 type barrels.	CCR4-NOT complex subunit 2/3/5, C-terminal domain	CATH (4.3.0)
C	2.30.30.1020	Mainly Beta	Roll	SH3 type barrels.	CCR4-NOT complex subunit 2/3/5, C-terminal domain	CATH (4.3.0)
E	2.30.30.1020	Mainly Beta	Roll	SH3 type barrels.	CCR4-NOT complex subunit 2/3/5, C-terminal domain	CATH (4.3.0)
B	2.30.30.1020	Mainly Beta	Roll	SH3 type barrels.	CCR4-NOT complex subunit 2/3/5, C-terminal domain	CATH (4.3.0)
D	1.25.40.790	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.25.40.800	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.40.790	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.40.800	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF04153	NOT2/NOT3/NOT5 C-terminal (NOT2_3_5_C)	NOT2/NOT3/NOT5 C-terminal	NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This entry represents the C-terminal SH3-like domain of NOT2, NOT3 and NOT5, which mediate heterodimerization and NO ...	NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This entry represents the C-terminal SH3-like domain of NOT2, NOT3 and NOT5, which mediate heterodimerization and NOT-module assembly [2,3].	Domain
B, E	PF04153	NOT2/NOT3/NOT5 C-terminal (NOT2_3_5_C)	NOT2/NOT3/NOT5 C-terminal	NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This entry represents the C-terminal SH3-like domain of NOT2, NOT3 and NOT5, which mediate heterodimerization and NO ...	NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This entry represents the C-terminal SH3-like domain of NOT2, NOT3 and NOT5, which mediate heterodimerization and NOT-module assembly [2,3].	Domain
A, D	PF04054	CCR4-Not complex component, Not1 (Not1)	CCR4-Not complex component, Not1	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5	-	regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA regulation of metabolic process RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability cellular process regulation of mRNA metabolic process deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay nuclear-transcribed mRNA poly(A) tail shortening transcription elongation by RNA polymerase II nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic process regulation of DNA-templated transcription protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex P-body protein-containing complex CCR4-NOT complex CCR4-NOT core complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex P-body protein-containing complex CCR4-NOT complex CCR4-NOT core complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, E	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2	-	regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA regulation of metabolic process RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability cellular process regulation of mRNA metabolic process deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay cellular response to stimulus sexual reproduction response to stimulus reproductive process response to pheromone conjugation with cellular fusion cellular response to pheromone response to pheromone triggering conjugation with cellular fusion cellular response to chemical stimulus response to chemical nuclear-transcribed mRNA poly(A) tail shortening transcription elongation by RNA polymerase II nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cell cycle regulation of cell cycle protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex CCR4-NOT complex CCR4-NOT core complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A, D	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1	ATPase activator activity molecular function activator activity molecular function regulator activity molecular adaptor activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process pseudohyphal growth growth growth of unicellular organism as a thread of attached cells filamentous growth cell growth filamentous growth of a population of unicellular organisms nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process regulation of cellular component organization negative regulation of cytoplasmic mRNA processing body assembly regulation of cytoplasmic mRNA processing body assembly membraneless organelle assembly negative regulation of organelle assembly cellular component biogenesis cellular component organization cellular component assembly cellular component organization or biogenesis organelle assembly negative regulation of cellular component organization P-body assembly regulation of cellular component biogenesis regulation of organelle organization organelle organization negative regulation of organelle organization regulation of organelle assembly cellular response to stimulus sexual reproduction response to stimulus reproductive process response to pheromone conjugation with cellular fusion cellular response to pheromone response to pheromone triggering conjugation with cellular fusion cellular response to chemical stimulus response to chemical transcription elongation by RNA polymerase II nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic process cell cycle regulation of cell cycle	cellular anatomical structure intracellular anatomical structure cytoplasm cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body protein-containing complex CCR4-NOT complex CCR4-NOT core complex cellular anatomical structure intracellular anatomical structure cytoplasm cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body protein-containing complex CCR4-NOT complex CCR4-NOT core complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR012270	CCR4-NOT complex, subunit 3/ 5	Family
C, F	IPR007282	NOT2/NOT3/NOT5, C-terminal	Domain
C, F	IPR007207	CCR4-Not complex component, Not N-terminal domain	Domain
C, F	IPR038635	CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily	Homologous Superfamily
C, F	IPR040168	Not2/Not3/Not5	Family
B, E	IPR007282	NOT2/NOT3/NOT5, C-terminal	Domain
B, E	IPR038635	CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily	Homologous Superfamily
B, E	IPR040168	Not2/Not3/Not5	Family
A, D	IPR032195	CCR4-NOT transcription complex subunit 1, HEAT repeat 1	Domain
A, D	IPR024557	CCR4-NOT transcription complex subunit 1, domain 4	Domain
A, D	IPR032191	CCR4-NOT transcription complex subunit 1, CAF1-binding domain	Domain
A, D	IPR032193	CCR4-NOT transcription complex subunit 1, TTP binding domain	Domain
A, D	IPR038535	CCR4-NOT subunit 1, TTP binding domain superfamily	Homologous Superfamily
A, D	IPR040398	CCR4-NOT transcription complex subunit 1	Family
A, D	IPR055454	CCR4-NOT transcription complex subunit 1-like, NOT1 connector	Domain
A, D	IPR007196	CCR4-Not complex component, Not1, C-terminal	Domain
A, D	IPR032194	CCR4-NOT transcription complex subunit 1, HEAT repeat	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.