2DNL | pdb_00002dnl

Solution structure of RNA binding domain in Cytoplasmic polyadenylation element binding protein 3

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	SCOP2 Family	Canonical RBD	8045472	4000236	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RNA-binding domain, RBD	8090278	3000110	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)
A	RRM_1_3	e2dnlA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16367	RNA recognition motif (RRM_7)	RNA recognition motif		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	cytoplasmic polyadenylation element binding protein 3	mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding mRNA 3'-UTR AU-rich region binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity translation factor activity translation factor activity, RNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding mRNA 3'-UTR AU-rich region binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity translation factor activity translation factor activity, RNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding RNA stem-loop binding	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process regulation of translational elongation negative regulation of cytoplasmic translational elongation negative regulation of translational elongation regulation of cytoplasmic translational elongation translational elongation cytoplasmic translational elongation 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 positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay nucleobase-containing compound catabolic process 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 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of cellular process RNA destabilization nuclear-transcribed mRNA catabolic process 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 3'-UTR-mediated mRNA destabilization multicellular organismal process regulation of developmental process cellular developmental process cell projection organization positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development cellular component organization positive regulation of developmental process neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process dendritic spine development plasma membrane bounded cell projection organization nervous system development generation of neurons neuron development positive regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening behavior system process learning or memory long-term memory nervous system process cognition memory positive regulation of protein metabolic process positive regulation of translation positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of gene expression cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to stimulus response to chemical response to amino acid regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication 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	midbody cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection midbody cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen CCR4-NOT complex protein-containing complex intracellular protein-containing complex synapse cell junction postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse apical dendrite

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038446	CEBP, ZZ domain superfamily	Homologous Superfamily
A	IPR000504	RNA recognition motif domain	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR032296	Cytoplasmic polyadenylation element-binding protein, ZZ domain	Domain
A	IPR034819	Cytoplasmic polyadenylation element-binding protein	Family
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8NE35	astrocytic tumor breast cancer large cell medulloblastoma lung carcinoma malignant glioma osteosarcoma pilocytic astrocytoma attention deficit hyperactivity disorder, inattentive type glioblastoma limb-girdle muscular dystrophy malignant colon neoplasm medulloblastoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor astrocytic tumor breast cancer large cell medulloblastoma lung carcinoma malignant glioma osteosarcoma pilocytic astrocytoma attention deficit hyperactivity disorder, inattentive type glioblastoma limb-girdle muscular dystrophy malignant colon neoplasm medulloblastoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor hepatocellular carcinoma lung cancer malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma

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.