3D3K

Crystal structure of human Edc3p

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	YjeF N-terminal domain-like	8054234	3000851	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjeF N-terminal domain-like	8054234	3000851	SCOP2B (2022-06-29)
C	SCOP2 Family	YjeF N-terminal domain-like	8045046	4003429	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	YjeF N-terminal domain-like	8054234	3000851	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	YjeF N-terminal domain-like	8054234	3000851	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	YjeF_N	e3d3kA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: YjeF_N	ECOD (1.6)
B	YjeF_N	e3d3kB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: YjeF_N	ECOD (1.6)
C	YjeF_N	e3d3kC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: YjeF_N	ECOD (1.6)
D	YjeF_N	e3d3kD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: YjeF_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
B	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
C	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
D	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
A, B, C, D	PF03853	YjeF-related protein N-terminus (YjeF_N)	YjeF-related protein N-terminus	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be ...	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128) [1], where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Enhancer of mRNA-decapping protein 3	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding identical protein binding protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle 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 cellular nitrogen compound metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle 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 cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process aromatic compound catabolic process negative regulation of cellular biosynthetic process cellular nitrogen compound catabolic 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 heterocycle catabolic 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 nitrogen compound metabolic 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 aromatic compound metabolic 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 organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle cytoplasmic ribonucleoprotein granule cellular anatomical entity cytoplasm supramolecular complex non-membrane-bounded organelle ribonucleoprotein granule membrane cytosol P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR047575	Sm domain	Domain
A, B, C, D	IPR034107	Lsm16, N-terminal	Domain
A, B, C, D	IPR025762	DFDF domain	Domain
A, B, C, D	IPR025609	Lsm14-like, N-terminal	Domain
A, B, C, D	IPR036652	YjeF N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR004443	YjeF N-terminal domain	Domain
A, B, C, D	IPR019050	FDF domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q96F86	intellectual disability, autosomal recessive 50 cleft lip hypertensive disorder MENTAL RETARDATION, AUTOSOMAL RECESSIVE 50 intellectual disability systemic sclerosis

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.