5ONA

Drosophila Bag-of-marbles CBM peptide bound to human CAF40-CNOT1

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	Not1 3-helical bundle-like	8090046	3002412	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Not1 3-helical bundle-like	8090046	3002412	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8090035	3000116	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ARM repeat-like	8090035	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)
A	DUF3819	e5onaA1	A: alpha bundles	X: CNOT9 binding domain CN9BD (DUF3819) (From Topology)	H: CNOT9 binding domain CN9BD (DUF3819) (From Topology)	T: CNOT9 binding domain CN9BD (DUF3819)	F: DUF3819	ECOD (1.6)
D	DUF3819	e5onaD1	A: alpha bundles	X: CNOT9 binding domain CN9BD (DUF3819) (From Topology)	H: CNOT9 binding domain CN9BD (DUF3819) (From Topology)	T: CNOT9 binding domain CN9BD (DUF3819)	F: DUF3819	ECOD (1.6)
B	Rcd1	e5onaB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Rcd1	ECOD (1.6)
E	Rcd1	e5onaE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Rcd1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
E	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF12842	CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 (DUF3819)	CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819	This is an uncharacterised domain that is found on the CCR4-Not complex component Not1. Not1 is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [1].	Domain
B, E	PF04078	Cell differentiation family, Rcd1-like (Rcd1)	Cell differentiation family, Rcd1-like	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Protein bag-of-marbles	mRNA 3'-UTR binding RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding protein binding ubiquitin binding ubiquitin-like protein binding translation regulator activity mRNA regulatory element binding translation repressor activity translation regulator activity, nucleic acid binding translation repressor activity	developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction asymmetric cell division gamete generation cell differentiation anatomical structure development germ cell development cellular process developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction asymmetric cell division gamete generation cell differentiation anatomical structure development germ cell development cellular process cell division cystoblast division cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway peptidoglycan recognition protein signaling pathway positive regulation of immune response response to bacterium regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of peptidoglycan recognition protein signaling pathway regulation of innate immune response response to external stimulus negative regulation of defense response to bacterium regulation of response to stimulus defense response to other organism negative regulation of response to external stimulus regulation of pattern recognition receptor signaling pathway positive regulation of defense response negative regulation of defense response activation of innate immune response regulation of immune response activation of immune response 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 signaling negative regulation of signaling positive regulation of biological process negative regulation of cell communication positive regulation of response to stimulus defense response to bacterium positive regulation of response to external stimulus negative regulation of peptidoglycan recognition protein signaling pathway immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response negative regulation of cellular process response to external biotic stimulus regulation of defense response to bacterium regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication spermatogenesis male gamete generation cellular biosynthetic process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic 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 macromolecule metabolic process regulation of metabolic process spermatogonial cell division oogenesis female gamete generation regulation of developmental process regulation of cell differentiation positive regulation of developmental process positive regulation of stem cell differentiation stem cell differentiation positive regulation of cell differentiation regulation of stem cell differentiation positive regulation of cellular process multicellular organismal process germ-line stem cell population maintenance maintenance of cell number stem cell population maintenance cell population proliferation germarium-derived egg chamber formation anatomical structure morphogenesis germ-line cyst formation anatomical structure formation involved in morphogenesis germarium-derived female germ-line cyst formation female germ-line cyst formation stem cell division germ-line stem cell division protein deubiquitination regulation of protein modification process positive regulation of protein metabolic process positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process protein modification by small protein removal positive regulation of macromolecule metabolic process protein modification process regulation of protein modification by small protein conjugation or removal regulation of protein K63-linked deubiquitination positive regulation of protein K63-linked deubiquitination positive regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein K63-linked deubiquitination positive regulation of protein deubiquitination regulation of protein deubiquitination macromolecule modification post-translational protein modification protein modification by small protein conjugation or removal positive regulation of cell communication positive regulation of signal transduction positive regulation of smoothened signaling pathway regulation of smoothened signaling pathway cell surface receptor signaling pathway smoothened signaling pathway positive regulation of signaling multicellular organism development regulation of growth growth cell competition in a multicellular organism symmetric stem cell division germline stem cell symmetric division symmetric cell division male germline stem cell symmetric division cellular component organization fusome organization organelle organization cellular component organization or biogenesis asymmetric stem cell division female germ-line stem cell asymmetric division germline stem cell asymmetric division	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle spectrosome cytoplasm cellular anatomical entity non-membrane-bounded organelle fusome
A, D	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 negative regulation of biological process negative regulation of cellular metabolic process regulation of primary 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 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 negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic 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 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 positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic 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 negative regulation of intracellular signal transduction regulation of retinoic acid receptor signaling pathway regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction negative regulation of cell communication cell communication cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction signal transduction cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus response to endogenous stimulus negative regulation of retinoic acid receptor signaling pathway retinoic acid receptor signaling pathway negative regulation of signal transduction cellular response to chemical stimulus regulation of response to stimulus response to chemical regulation of cell communication nuclear receptor-mediated signaling pathway response to lipid negative regulation of intracellular steroid hormone receptor signaling pathway response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound negative regulation of intracellular estrogen receptor signaling pathway steroid hormone receptor signaling pathway cellular response to organic cyclic compound estrogen receptor signaling pathway cellular response to lipid negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic 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, E	CCR4-NOT transcription complex subunit 9	protein binding binding kinase binding enzyme binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity epidermal growth factor receptor binding signaling receptor binding growth factor receptor binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein binding binding kinase binding enzyme binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity epidermal growth factor receptor binding signaling receptor binding growth factor receptor binding transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular response to cytokine stimulus signal transduction regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process primary metabolic process translation regulation of translation developmental process reproductive process sex differentiation developmental process involved in reproduction intracellular receptor signaling pathway response to lipid negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction negative regulation of cell communication negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound negative regulation of intracellular estrogen receptor signaling pathway steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus response to endogenous stimulus cellular response to organic cyclic compound negative regulation of signal transduction estrogen receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus cellular response to lipid regulation of cell communication nuclear receptor-mediated signaling pathway 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 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 positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of cellular metabolic process positive regulation of phosphate metabolic process peptidyl-serine modification positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of protein phosphorylation phosphorus metabolic process protein modification process positive regulation of cellular process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation positive regulation of cell communication positive regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway ERBB signaling pathway positive regulation of signaling	CCR4-NOT complex protein-containing complex intracellular protein-containing complex membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle supramolecular complex CCR4-NOT complex protein-containing complex intracellular protein-containing complex membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle CCR4-NOT core complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR007196	CCR4-Not complex component, Not1, C-terminal	Domain
A, D	IPR032194	CCR4-NOT transcription complex subunit 1, HEAT repeat	Domain
B, E	IPR016024	Armadillo-type fold	Homologous Superfamily
B, E	IPR011989	Armadillo-like helical	Homologous Superfamily
B, E	IPR007216	CCR4-NOT transcription complex subunit 9	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: A5YKK6	atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma spina bifida autism spectrum disorder malignant ependymoma ovarian cancer holoprosencephaly medulloblastoma psoriasis
B, E	Pharos: Q92600	breast cancer lung cancer large cell medulloblastoma ovarian cancer lung adenocarcinoma psoriasis

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.