1UW4 | pdb_00001uw4

The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1uw4b_	All alpha proteins	alpha-alpha superhelix	ARM repeat	MIF4G domain-like	Regulator of nonsense transcripts 2, UPF2	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1uw4d_	All alpha proteins	alpha-alpha superhelix	ARM repeat	MIF4G domain-like	Regulator of nonsense transcripts 2, UPF2	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1uw4a_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Smg-4/UPF3	RNA processing protein UPF3x, RRM domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1uw4c_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Smg-4/UPF3	RNA processing protein UPF3x, RRM domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	MA3 domain-like	8022811	4000569	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	ARM repeat-like	8035191	3000116	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	ARM repeat-like	8035191	3000116	SCOP2B (2022-06-29)
A	SCOP2 Family	Smg-4/UPF3-like	8022806	4001467	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RNA-binding domain, RBD	8035186	3000110	SCOP2 (2022-06-29)
C	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)
B		e1uw4B1	A: Repetitive alpha hairpins	X: ARM repeat	H: ARM repeat	T: MIF4G	F:	ECOD (20:10:01)
D		e1uw4D1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
A		e1uw4A1	A: Alpha-beta plaits	X: RNA-binding domain, RBD	H: RNA-binding domain, RBD	T: Smg4_UPF3	F:	ECOD (20:10:01)
C		e1uw4C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
C	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
B, D	PF02854	MIF4G domain (MIF4G)	MIF4G domain	-	Repeat
A, C	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	REGULATOR OF NONSENSE TRANSCRIPTS 2	RNA binding binding nucleic acid binding sequence-specific DNA binding DNA binding telomeric 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 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, C	UPF3X	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 developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular developmental process regulation of developmental process regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process neurogenesis neuron differentiation positive regulation of cell differentiation cell differentiation generation of neurons regulation of neuron differentiation 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 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 mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process positive regulation of mRNA cis splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing regulation of mRNA cis splicing, via spliceosome regulation of RNA metabolic process RNA processing regulation of nucleobase-containing compound metabolic process 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 regulation of mRNA metabolic process 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 plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development neuron 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 centrosome microtubule organizing center cytoskeleton centriolar satellite microtubule cytoskeleton cytoplasm cytosol protein-containing complex exon-exon junction complex nuclear protein-containing complex somatodendritic compartment cell body neuronal cell body nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: 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

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.