4B8A | pdb_00004b8a

Structure of yeast NOT1 MIF4G domain co-crystallized with CAF1

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)
B	d4b8ab1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	CAF1-like ribonuclease	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4b8ab2	Artifacts	Tags	Tags	Tags	N-terminal Tags	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ribonuclease H-like	8041933	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8053826	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)
B	CAF1	e4b8aB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: CAF1	ECOD (1.6)
A	CNOT1_CAF1_bind	e4b8aA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CNOT1_CAF1_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.25.40.180	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
B	PF04857	CAF1 family ribonuclease (CAF1)	CAF1 family ribonuclease	-	Family
A	PF16415	CCR4-NOT transcription complex subunit 1 CAF1-binding domain (CNOT1_CAF1_bind)	CCR4-NOT transcription complex subunit 1 CAF1-binding domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	POLY(A) RIBONUCLEASE POP2	3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	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 nuclear-transcribed mRNA poly(A) tail shortening 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 regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic 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 negative regulation of cellular process 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 macromolecule biosynthetic process mRNA metabolic 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 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 projection cellular anatomical structure mating projection cell tip mating projection tip cell pole plasma membrane bounded cell projection site of polarized growth intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle cell projection cellular anatomical structure mating projection cell tip mating projection tip cell pole plasma membrane bounded cell projection site of polarized growth intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle 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
A	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1	ATPase activator activity molecular function activator activity molecular function regulator activity ATPase 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
B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B	IPR039637	CCR4-NOT transcription complex subunit 7/8/Pop2	Family
B	IPR006941	Ribonuclease CAF1	Family
B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR032195	CCR4-NOT transcription complex subunit 1, HEAT repeat 1	Domain
A	IPR024557	CCR4-NOT transcription complex subunit 1, domain 4	Domain
A	IPR032191	CCR4-NOT transcription complex subunit 1, CAF1-binding domain	Domain
A	IPR032193	CCR4-NOT transcription complex subunit 1, TTP binding domain	Domain
A	IPR038535	CCR4-NOT subunit 1, TTP binding domain superfamily	Homologous Superfamily
A	IPR040398	CCR4-NOT transcription complex subunit 1	Family
A	IPR055454	CCR4-NOT transcription complex subunit 1-like, NOT1 connector	Domain
A	IPR007196	CCR4-Not complex component, Not1, C-terminal	Domain
A	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.