4A54

Structural basis of the Dcp1:Dcp2 mRNA decapping complex activation by Edc3 and Scd6

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	LSM14 N-terminal domain-like	8045048	4001796	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sm-like ribonucleoproteins	8054233	3000419	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	KOG2585	e4a54A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2585	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09532	FDF domain (FDF)	FDF domain	The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops [1]. It is found at the C terminus of Scd6p-like SM domains [1][2]. It is also found with other dive ...	The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops [1]. It is found at the C terminus of Scd6p-like SM domains [1][2]. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	EDC3	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance biosynthetic process RNA catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-independent decay mRNA catabolic process 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 regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance biosynthetic process RNA catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-independent decay mRNA catabolic process 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 nucleobase-containing compound catabolic process organic cyclic compound metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process RNA decapping catabolic process cellular biosynthetic process RNA metabolic process macromolecule catabolic process organic substance metabolic process deadenylation-independent decapping of nuclear-transcribed mRNA negative regulation of cellular process mRNA methylguanosine-cap decapping negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process biological regulation regulation of macromolecule metabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process organic substance catabolic process 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	intracellular anatomical structure cytoplasmic ribonucleoprotein granule cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule P-body
B	MRNA DECAPPING COMPLEX SUBUNIT 2	RNA binding mRNA cap binding binding organic cyclic compound binding nucleic acid binding RNA cap binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding single-stranded RNA binding RNA binding mRNA cap binding binding organic cyclic compound binding nucleic acid binding RNA cap binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding single-stranded RNA binding magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding pyrophosphatase activity 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process 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 organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process 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 organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA regulation of metabolic process RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization organic substance metabolic process regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability cellular process regulation of mRNA metabolic process organic substance catabolic process mRNA processing RNA processing nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	intracellular anatomical structure cytoplasmic ribonucleoprotein granule cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule cytosol protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule cytosol protein-containing complex RNA decapping complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR047575	Sm domain	Domain
A	IPR034107	Lsm16, N-terminal	Domain
A	IPR025762	DFDF domain	Domain
A	IPR036652	YjeF N-terminal domain superfamily	Homologous Superfamily
A	IPR004443	YjeF N-terminal domain	Domain
A	IPR019050	FDF domain	Domain
B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
B	IPR036189	mRNA decapping protein 2, Box A domain superfamily	Homologous Superfamily
B	IPR007722	mRNA decapping protein 2, Box A domain	Domain
B	IPR044099	mRNA decapping enzyme 2 , NUDIX hydrolase domain	Domain
B	IPR000086	NUDIX hydrolase domain	Domain
B	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

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.