4GMJ

Structure of human NOT1 MIF4G domain co-crystallized with CAF1

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ARM repeat-like	8053825	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8053825	3000116	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ARM repeat-like	8053825	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8033733	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8033733	3000143	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribonuclease H-like	8033733	3000143	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)
A	CNOT1_CAF1_bind	e4gmjA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CNOT1_CAF1_bind	ECOD (1.6)
C	CNOT1_CAF1_bind	e4gmjC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CNOT1_CAF1_bind	ECOD (1.6)
E	CNOT1_CAF1_bind	e4gmjE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CNOT1_CAF1_bind	ECOD (1.6)
B	CAF1	e4gmjB1	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)
D	CAF1	e4gmjD1	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)
F	CAF1	e4gmjF1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF16415	CCR4-NOT transcription complex subunit 1 CAF1-binding domain (CNOT1_CAF1_bind)	CCR4-NOT transcription complex subunit 1 CAF1-binding domain	-	Repeat
B, D, F	PF04857	CAF1 family ribonuclease (CAF1)	CAF1 family ribonuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	CCR4-NOT transcription complex subunit 1	protein binding binding protein domain specific binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA binding organic cyclic compound binding nucleic acid binding armadillo repeat domain binding molecular adaptor activity nuclear estrogen receptor binding	developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number stem cell population maintenance regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number stem cell population maintenance regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation 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 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 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 nucleobase-containing compound metabolic 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 organic cyclic compound 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 nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound catabolic 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 organic substance catabolic process positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay trophectodermal cell differentiation cellular developmental process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development positive regulation of nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of cytoplasmic mRNA processing body assembly regulation of cytoplasmic mRNA processing body assembly non-membrane-bounded organelle assembly cellular component biogenesis cellular component organization cellular component assembly cellular component organization or biogenesis positive regulation of cellular process organelle assembly P-body assembly positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of organelle organization organelle organization regulation of organelle assembly positive regulation of organelle assembly cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling negative regulation of signaling regulation of retinoic acid receptor signaling pathway regulation of signal transduction negative regulation of cell communication cell communication signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of retinoic acid receptor signaling pathway retinoic acid receptor signaling pathway negative regulation of signal transduction regulation of response to stimulus regulation of cell communication response to organic substance response to lipid intracellular estrogen receptor signaling pathway hormone-mediated signaling pathway negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway cellular response to organic substance cellular response to steroid hormone stimulus response to organic cyclic compound negative regulation of intracellular estrogen receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to organic cyclic compound cellular response to chemical stimulus steroid hormone mediated signaling pathway response to chemical cellular response to lipid nuclear receptor signaling pathway intracellular steroid hormone receptor signaling pathway negative regulation of RNA biosynthetic process DNA-templated transcription transcription by RNA polymerase II negative 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 organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing post-transcriptional gene silencing	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol CCR4-NOT complex protein-containing complex intracellular protein-containing complex membrane-bounded organelle peroxisome intracellular membrane-bounded organelle microbody membrane intracellular organelle bounding membrane of organelle membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol CCR4-NOT complex protein-containing complex intracellular protein-containing complex membrane-bounded organelle peroxisome intracellular membrane-bounded organelle microbody membrane intracellular organelle bounding membrane of organelle organelle peroxisomal membrane microbody organelle membrane cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle CCR4-NOT core complex extracellular region extracellular space nucleus
B, D, F	CCR4-NOT transcription complex subunit 7	3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding protein binding DNA-binding transcription factor binding poly(A)-specific ribonuclease activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process positive regulation of metabolic process post-transcriptional regulation of gene expression positive regulation of macromolecule metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression nucleic acid catabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process mRNA methylguanosine-cap decapping nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process organic cyclic compound catabolic 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 organic substance catabolic process cellular response to stimulus response to organic substance response to stimulus regulation of type I interferon-mediated signaling pathway response to cytokine regulation of signal transduction response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction immune response response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress innate immune response cellular response to organic substance response to external biotic stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction cellular response to chemical stimulus negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway immune system process type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response nuclear-transcribed mRNA poly(A) tail shortening positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay organonitrogen compound biosynthetic process protein metabolic process organonitrogen compound metabolic process regulation of protein metabolic process translation regulation of translation cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly non-membrane-bounded organelle assembly cellular component organization or biogenesis positive regulation of nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of cellular process regulatory ncRNA-mediated gene silencing negative regulation of cell population proliferation positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication defense response to virus response to virus positive regulation of macromolecule biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing miRNA-mediated post-transcriptional gene silencing post-transcriptional gene silencing cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation peptidyl-tyrosine modification regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process tyrosine phosphorylation of STAT protein protein phosphorylation regulation of tyrosine phosphorylation of STAT protein phosphorylation regulation of peptidyl-tyrosine phosphorylation macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol intracellular non-membrane-bounded organelle non-membrane-bounded organelle CCR4-NOT complex protein-containing complex intracellular protein-containing complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex P-body CCR4-NOT core complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR024557	CCR4-NOT transcription complex subunit 1, domain 4	Domain
A, C, E	IPR032191	CCR4-NOT transcription complex subunit 1, CAF1-binding domain	Domain
A, C, E	IPR032193	CCR4-NOT transcription complex subunit 1, TTP binding domain	Domain
A, C, E	IPR038535	CCR4-NOT subunit 1, TTP binding domain superfamily	Homologous Superfamily
A, C, E	IPR040398	CCR4-NOT transcription complex subunit 1	Family
A, C, E	IPR007196	CCR4-Not complex component, Not1, C-terminal	Domain
A, C, E	IPR032194	CCR4-NOT transcription complex subunit 1, HEAT repeat	Domain
B, D, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B, D, F	IPR039637	CCR4-NOT transcription complex subunit 7/8/Pop2	Family
B, D, F	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B, D, F	IPR006941	Ribonuclease CAF1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E	Pharos: A5YKK6	atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma spina bifida autism spectrum disorder malignant ependymoma ovarian cancer holoprosencephaly medulloblastoma psoriasis
B, D, F	Pharos: Q9UIV1	astrocytic tumor malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis breast cancer medulloblastoma ovarian cancer plasma cell myeloma tuberculosis lymphoplasmacytic lymphoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.