4C0D | pdb_00004c0d

Structure of the NOT module of the human CCR4-NOT complex (CNOT1-CNOT2-CNOT3)

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	8057081	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8057082	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NOT2_3_5 domain-like	8090759	3002454	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NOT2_3_5 domain-like	8090760	3002454	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	RNA_pol_I_A49	e4c0dA1	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)
C	NOT2_3_5_C	e4c0dC1	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	e4c0dB1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04054	CCR4-Not complex component, Not1 (Not1)	CCR4-Not complex component, Not1	-	Repeat
C	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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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
C	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3	-	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 multicellular organism development determination of bilateral symmetry anatomical structure development pattern specification process determination of left/right symmetry 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 multicellular organism development determination of bilateral symmetry anatomical structure development pattern specification process determination of left/right symmetry left/right pattern formation regionalization specification of symmetry regulation of biosynthetic process regulation of cellular process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process homeostatic process positive regulation of biological process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription catabolic process macromolecule catabolic process RNA catabolic process mRNA catabolic process mRNA metabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression positive regulation of macromolecule metabolic process regulation of biological quality positive regulation of mRNA metabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process nuclear-transcribed mRNA catabolic process RNA destabilization regulation of 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 regulation of protein metabolic process translation protein biosynthetic process regulation of translation protein metabolic process trophectodermal cell differentiation cellular developmental process chordate embryonic development embryo development in utero embryonic development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching cell differentiation anatomical structure formation involved in morphogenesis blastocyst development	CCR4-NOT complex protein-containing complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex CCR4-NOT complex protein-containing complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body CCR4-NOT core complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	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 biosynthetic process regulation of cellular process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule 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 biosynthetic process regulation of cellular process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process 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 positive regulation of biological process membraneless 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 response to lipid signaling 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 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 signal transduction 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 cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus response to endogenous stimulus negative regulation of signal transduction estrogen receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus response to chemical cellular response to lipid regulation of cell communication nuclear receptor-mediated signaling pathway 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 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 nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic 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 RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription regulation of protein metabolic process translation protein biosynthetic process regulation of translation protein metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process 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	CCR4-NOT complex protein-containing complex intracellular protein-containing complex cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle CCR4-NOT complex protein-containing complex intracellular protein-containing complex cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body CCR4-NOT core complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR024557	CCR4-NOT transcription complex subunit 1, domain 4	Domain
A	IPR055104	CCR4-NOT transcription complex subunit 1, N-terminal domain	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
C	IPR012270	CCR4-NOT complex, subunit 3/ 5	Family
C	IPR007282	NOT2/NOT3/NOT5, C-terminal	Domain
C	IPR007207	CCR4-Not complex component, Not N-terminal domain	Domain
C	IPR038635	CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily	Homologous Superfamily
C	IPR040168	Not2/Not3/Not5	Family
B	IPR007282	NOT2/NOT3/NOT5, C-terminal	Domain
B	IPR038635	CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily	Homologous Superfamily
B	IPR040168	Not2/Not3/Not5	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: A5YKK6	atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma spina bifida autism spectrum disorder malignant ependymoma ovarian cancer holoprosencephaly medulloblastoma psoriasis
C	Pharos: O75175	acute T cell leukemia Precursor T-Cell Lymphoblastic Leukemia-Lymphoma prostate cancer glioblastoma lung cancer malignant mesothelioma alcoholic liver cirrhosis intellectual disability malignant ependymoma medulloblastoma primitive neuroectodermal tumor Takayasu arteritis atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma acute T cell leukemia Precursor T-Cell Lymphoblastic Leukemia-Lymphoma prostate cancer glioblastoma lung cancer malignant mesothelioma alcoholic liver cirrhosis intellectual disability malignant ependymoma medulloblastoma primitive neuroectodermal tumor Takayasu arteritis atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma osteosarcoma
B	Pharos: Q9NZN8	astrocytic tumor glioblastoma pancreatic intraductal papillary-mucinous carcinoma testicular germ cell tumor dermatomyositis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm esophageal adenocarcinoma pancreatic ductal adenocarcinoma Sjogren syndrome

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.