Annotations: 7NWU

Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII

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)
H	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA-binding domain, RBD	8035186	3000110	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RNA-binding domain, RBD	8035186	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain, RBD	8035186	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8035186	3000110	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)
H	Thaumatin	e7nwuH1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
F	Thaumatin	e7nwuF1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
D	Thaumatin	e7nwuD1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
B	Thaumatin	e7nwuB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
G	AAA_lid_RFC1	e7nwuG1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)
E	zf-NPL4	e7nwuE1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: zf-NPL4	ECOD (v295.2)
C	zf-NPL4	e7nwuC1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: zf-NPL4	ECOD (v295.2)
A	AAA_lid_RFC1	e7nwuA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: AAA_lid_RFC1	ECOD (v295.2)

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 (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF02854	MIF4G domain (MIF4G)	MIF4G domain	-	Repeat
A, C, E, G	PF03467	Smg-4/UPF3 family (Smg4_UPF3)	Smg-4/UPF3 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Regulator of nonsense transcripts 2	sequence-specific DNA binding DNA binding binding nucleic acid binding telomeric repeat DNA binding RNA binding	regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process regulation of biological process regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic 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 negative regulation of RNA metabolic process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process nuclear-transcribed mRNA catabolic process negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay biological regulation negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biosynthetic process positive regulation of gene expression cellular process regulation of mRNA metabolic process cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization positive regulation of mRNA metabolic process positive regulation of RNA metabolic process positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay positive regulation of catabolic process positive regulation of mRNA catabolic process RNA surveillance	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm membrane-bounded organelle intracellular organelle protein-containing complex organelle nucleus exon-exon junction complex nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm membrane-bounded organelle intracellular organelle protein-containing complex organelle nucleus exon-exon junction complex nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex nonsense-mediated decay complex
A, C, E, G	Regulator of nonsense transcripts 3B	RNA binding binding nucleic acid binding mRNA binding	regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process nucleobase-containing compound metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay catabolic process RNA metabolic process macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process nuclear-transcribed mRNA catabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay positive regulation of catabolic process positive regulation of mRNA catabolic process negative regulation of biosynthetic process regulation of mRNA metabolic process RNA surveillance	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol protein-containing complex exon-exon junction complex nuclear protein-containing complex somatodendritic compartment cell body neuronal cell body catalytic complex nonsense-mediated decay complex nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR016024	Armadillo-type fold	Homologous Superfamily
B, D, F, H	IPR039762	Nonsense-mediated mRNA decay protein Nmd2/UPF2	Family
B, D, F, H	IPR007193	Up-frameshift suppressor 2, C-terminal	Domain
B, D, F, H	IPR003890	MIF4G-like, type 3	Domain
A, C, E, G	IPR034979	UPF3B, RNA recognition motif-like domain	Domain
A, C, E, G	IPR039722	Nonsense-mediated mRNA decay protein 3	Family
A, C, E, G	IPR005120	UPF3 domain	Domain
A, C, E, G	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, C, E, G	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	: Q9BZI7	syndromic X-linked intellectual disability 14 FG syndrome autism, susceptibility to, X-linked 2 intellectual disability adrenal cortex carcinoma lung cancer Mental Retardation, X-Linked 1 malignant mesothelioma Pick disease thoracic aortic aneurysm dermatomyositis progressive supranuclear palsy X-linked intellectual disability with marfanoid habitus