4CQO | pdb_00004cqo

Structure of the human CNOT1 superfamily homology domain in complex with a Nanos1 peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
C	SCOP2B Superfamily	ARM repeat-like	8057081	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8057082	3000116	SCOP2B (2022-06-29)
A	SCOP2 Family	Not1-like	8045230	4004363	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8057081	3000116	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8057082	3000116	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)
C		e4cqoC1	A: Glycosyl hydrolase domain-like	X: alpha/alpha toroid	H: alpha/alpha toroid	T: Tsi3	F:	ECOD (20:10:01)
A		e4cqoA1	A: Glycosyl hydrolase domain-like	X: alpha/alpha toroid	H: alpha/alpha toroid	T: Tsi3	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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
B, D	NANOS HOMOLOG 1	RNA binding binding nucleic acid binding mRNA binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity translation regulator activity translation repressor activity cation binding transition metal ion binding zinc ion binding ion binding RNA binding binding nucleic acid binding mRNA binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity translation regulator activity translation repressor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	multicellular organismal process cellular developmental process central nervous system neuron development cell development cerebellar neuron development multicellular organism development central nervous system neuron differentiation neurogenesis neuron differentiation metencephalon development cell differentiation anatomical structure development system development developmental process multicellular organismal process cellular developmental process central nervous system neuron development cell development cerebellar neuron development multicellular organism development central nervous system neuron differentiation neurogenesis neuron differentiation metencephalon development cell differentiation anatomical structure development system development developmental process head development animal organ development brain development nervous system development generation of neurons cerebellum development central nervous system development neuron development cellular process hindbrain development 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 macromolecule metabolic process regulation of metabolic process sexual reproduction reproductive process oogenesis multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation germ cell development epithelium migration tissue migration ameboidal-type cell migration epithelial cell migration cell migration cell motility multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis 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 positive regulation of RNA metabolic process nucleic acid catabolic process catabolic process positive regulation of biological process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process positive regulation of cellular 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	cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm
A, C	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 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 negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression 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 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 protein metabolic process negative regulation of metabolic process 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 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 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 membraneless organelle assembly cellular component biogenesis cellular component organization cellular component assembly cellular component organization or biogenesis 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 negative regulation of intracellular estrogen receptor signaling pathway steroid hormone receptor signaling pathway 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	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex P-body CCR4-NOT core complex extracellular region extracellular space nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR008705	Nanos/Xcat2	Family
B, D	IPR038129	Nanos domain superfamily	Homologous Superfamily
B, D	IPR024161	Zinc finger, nanos-type	Domain
A, C	IPR024557	CCR4-NOT transcription complex subunit 1, domain 4	Domain
A, C	IPR055104	CCR4-NOT transcription complex subunit 1, N-terminal domain	Domain
A, C	IPR032191	CCR4-NOT transcription complex subunit 1, CAF1-binding domain	Domain
A, C	IPR032193	CCR4-NOT transcription complex subunit 1, TTP binding domain	Domain
A, C	IPR038535	CCR4-NOT subunit 1, TTP binding domain superfamily	Homologous Superfamily
A, C	IPR040398	CCR4-NOT transcription complex subunit 1	Family
A, C	IPR055454	CCR4-NOT transcription complex subunit 1-like, NOT1 connector	Domain
A, C	IPR007196	CCR4-Not complex component, Not1, C-terminal	Domain
A, C	IPR032194	CCR4-NOT transcription complex subunit 1, HEAT repeat	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q8WY41	spermatogenic failure 12 malignant mesothelioma pituitary cancer adrenal cortex carcinoma cystic fibrosis juvenile dermatomyositis male infertility with azoospermia or oligozoospermia due to single gene mutation osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia amyotrophic lateral sclerosis Duchenne muscular dystrophy large cell medulloblastoma male infertility with teratozoospermia due to single gene mutation medulloblastoma ovarian cancer spermatogenic failure 12 malignant mesothelioma pituitary cancer adrenal cortex carcinoma cystic fibrosis juvenile dermatomyositis male infertility with azoospermia or oligozoospermia due to single gene mutation osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia amyotrophic lateral sclerosis Duchenne muscular dystrophy large cell medulloblastoma male infertility with teratozoospermia due to single gene mutation medulloblastoma ovarian cancer pilocytic astrocytoma azoospermia Emery-Dreifuss muscular dystrophy limb-girdle muscular dystrophy malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm
A, C	Pharos: A5YKK6	atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma spina bifida autism spectrum disorder malignant ependymoma ovarian cancer holoprosencephaly medulloblastoma 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.