2WJV | pdb_00002wjv

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2

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)
C [auth D]	SCOP2 Family	UPF2 UPF1-binding region-like	8045223	4004361	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	UPF2 UPF1-binding region-like	8057069	3002386	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	RING/U-box like	8053236	3000160	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RING/U-box like	8053235	3000160	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8090880	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8090881	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RING/U-box like	8053235	3000160	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8090881	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RING/U-box like	8053236	3000160	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8090880	3002019	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)
D [auth E]	TED	e2wjvE1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: Pilus-presented adhesin helical insertion domain	T: Pilus-presented adhesin helical insertion domain	F: TED	ECOD (v294.1)
C [auth D]	Upf2	e2wjvD1	A: a/b three-layered sandwiches	X: Thiolase-like	H: Thiolase-like	T: Thiolase-like	F: Upf2	ECOD (v294.1)
B	HypA	e2wjvB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: HypA	ECOD (v294.1)
A	UPF1_Zn_bind	e2wjvA1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UPF1_Zn_bind	ECOD (v294.1)
A	AAA_11	e2wjvA3	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11	ECOD (v294.1)
A	UPF1_1B_dom	e2wjvA4	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UPF1_1B_dom	ECOD (v294.1)
A	AAA_12	e2wjvA5	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_12	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	6.10.250.770	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D [auth E]	4.10.80.160	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4		CATH (4.3.0)
C [auth D]	6.10.250.770	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C [auth D]	4.10.80.160	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4		CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.30.230	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	6.10.140.1240	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.230	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	6.10.140.1240	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], D [auth E]	PF04050	Up-frameshift suppressor 2 (Upf2)	Up-frameshift suppressor 2	-	Repeat
A, B	PF18141	RNA helicase UPF1, 1B domain (UPF1_1B_dom)	RNA helicase UPF1, 1B domain	UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. Together with UPF2 and UPF3, forms a surveillance complex, in which UPF2 acts as ...	UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. Together with UPF2 and UPF3, forms a surveillance complex, in which UPF2 acts as a bridge between UPF1 and UPF3. UPF2 and UPF3 are non-enzymatic components of the complex that stimulate the activity of UPF1 [1, 2]. UPF1 has a N-terminal cysteine/histidine-rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, followed by a helicase core that belongs to superfamily 1 (SF1). This entry represents 1B domain of UPF1 which has a regulatory role. It suffers conformational changes from an inhibitory state to a transition-state complex that modulate RNA binding [1, 2].	Domain
A, B	PF13086	AAA domain (AAA_11)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.	Domain
A, B	PF13087	AAA domain (AAA_12)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.	Domain
A, B	PF09416	RNA helicase (UPF2 interacting domain) (UPF1_Zn_bind)	RNA helicase (UPF2 interacting domain)	UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediat ...	UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], D [auth E]	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, B	REGULATOR OF NONSENSE TRANSCRIPTS 1	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity chromatin binding binding RNA binding nucleic acid binding sequence-specific DNA binding DNA binding telomeric repeat DNA binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity chromatin binding binding RNA binding nucleic acid binding sequence-specific DNA binding DNA binding telomeric repeat DNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity, acting on RNA RNA helicase activity ATP-dependent activity, acting on RNA cation binding transition metal ion binding zinc ion binding metal ion binding DNA helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA double-stranded DNA helicase activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of cellular process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic 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 regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process cell cycle phase transition cell cycle cell cycle process 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 establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to stimulus response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of cellular component organization protein-containing complex disassembly protein biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process cellular component organization post-transcriptional regulation of gene expression protein metabolic process translational termination cellular component organization or biogenesis cellular component disassembly protein-containing complex organization regulation of protein metabolic process regulation of translational termination translation regulation of translation 3'-UTR-mediated mRNA destabilization positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of mRNA metabolic process positive regulation of RNA metabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process regulation of telomere maintenance telomere organization chromosome organization regulation of chromosome organization regulation of organelle organization telomere maintenance organelle organization regulation of DNA metabolic process positive regulation of mRNA cis splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing positive regulation of macromolecule biosynthetic process regulation of mRNA cis splicing, via spliceosome RNA processing mRNA cis splicing, via spliceosome positive regulation of mRNA processing positive regulation of mRNA splicing, via spliceosome RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of mRNA processing RNA splicing nucleobase-containing compound biosynthetic process regulation of RNA splicing RNA splicing, via transesterification reactions positive regulation of gene expression mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile positive regulation of RNA splicing histone mRNA catabolic process histone mRNA metabolic process cellular response to stress DNA damage response response to stress DNA repair DNA-templated DNA replication nuclear DNA replication cell cycle DNA replication telomere maintenance via semi-conservative replication nuclear-transcribed mRNA catabolic process, nonsense-mediated decay response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1 cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex supraspliceosomal complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex supraspliceosomal complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome perinuclear region of cytoplasm exon-exon junction complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex P-body chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], D [auth E]	IPR016024	Armadillo-type fold	Homologous Superfamily
C [auth D], D [auth E]	IPR039762	Nonsense-mediated mRNA decay protein Nmd2/UPF2	Family
C [auth D], D [auth E]	IPR007193	Up-frameshift suppressor 2, C-terminal	Domain
C [auth D], D [auth E]	IPR003890	MIF4G-like, type 3	Domain
A, B	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
A, B	IPR018999	RNA helicase UPF1, Cys/His rich zinc-binding domain	Domain
A, B	IPR045055	DNA2/NAM7-like helicase	Family
A, B	IPR040812	RNA helicase UPF1, 1B domain	Domain
A, B	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR006935	Helicase/UvrB, N-terminal	Domain
A, B	IPR047187	Upf1-like, C-terminal helicase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q92900	breast carcinoma osteosarcoma ovarian cancer

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.

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