7QG6 | pdb_00007qg6

Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth B]	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA-binding domain, RBD	8088495	3000110	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RNA-binding domain, RBD	8088495	3000110	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RNA-binding domain, RBD	8088495	3000110	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	RNA-binding domain, RBD	8088495	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	Beta-lactamase2	e7qg6H1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Beta-lactamase2	ECOD (v294.1)
F	Beta-lactamase2	e7qg6F1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Beta-lactamase2	ECOD (v294.1)
D [auth B]	Beta-lactamase2	e7qg6B1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Beta-lactamase2	ECOD (v294.1)
B [auth D]	Beta-lactamase2	e7qg6D1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Beta-lactamase2	ECOD (v294.1)
A [auth C]		e7qg6C01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F:	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth B], F, H	PF02854	MIF4G domain (MIF4G)	MIF4G domain	-	Repeat
A [auth C], C [auth A], 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 [auth D], D [auth B], F, H	Regulator of nonsense transcripts 2	RNA binding binding nucleic acid binding sequence-specific DNA binding DNA binding telomeric repeat DNA binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization intercellular transport mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization cellular process metabolic process macromolecule metabolic process animal organ regeneration regeneration regulation of cellular process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule cytosol perinuclear region of cytoplasm membrane-bounded organelle protein-containing complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule cytosol perinuclear region of cytoplasm membrane-bounded organelle protein-containing complex nucleus exon-exon junction complex nuclear protein-containing complex intracellular membrane-bounded organelle
A [auth C], C [auth A], E, G	Regulator of nonsense transcripts 3A	RNA binding binding nucleic acid binding mRNA binding molecular sequestering activity protein sequestering activity sequence-specific DNA binding DNA binding telomeric repeat DNA 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 negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process negative regulation of metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process negative regulation of RNA metabolic process catabolic process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of catabolic process nuclear-transcribed mRNA catabolic process negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biosynthetic process regulation of mRNA metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport positive regulation of mRNA cis splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing regulation of mRNA cis splicing, via spliceosome RNA processing positive regulation of mRNA metabolic process positive regulation of RNA metabolic process mRNA cis splicing, via spliceosome positive regulation of mRNA processing positive regulation of mRNA splicing, via spliceosome RNA biosynthetic process nucleic acid biosynthetic process regulation of mRNA processing RNA splicing nucleobase-containing compound biosynthetic process regulation of RNA splicing RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile positive regulation of RNA splicing cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis random inactivation of X chromosome heterochromatin formation sex-chromosome dosage compensation epigenetic regulation of gene expression heterochromatin organization dosage compensation by inactivation of X chromosome negative regulation of gene expression, epigenetic multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	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 cell periphery plasma membrane membrane nucleoplasm cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], C [auth A], E, G	Pharos: Q9H1J1	nodular sclerosis classical Hodgkin lymphoma osteosarcoma psoriasis

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.