2GK6

Structural and Functional insights into the human Upf1 helicase core

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)
A	d2gk6a2	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Upf1 barrel domain-like	Upf1 barrel domain-like	Upf1 barrel domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2gk6a3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Upf1, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2gk6a1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Upf1, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2gk6a4	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2gk6b2	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Upf1 barrel domain-like	Upf1 barrel domain-like	Upf1 barrel domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2gk6b3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Upf1, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2gk6b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Upf1, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2gk6b4	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8090881	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Upf1 beta-barrel domain-like	8090878	3002168	SCOP2B (2022-06-29)
A	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)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8090880	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Upf1 beta-barrel domain-like	8090878	3002168	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	KOG1802	e2gk6A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: KOG1802	ECOD (1.6)
A	AAA_12	e2gk6A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_12	ECOD (1.6)
A	AAA_11	e2gk6A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11	ECOD (1.6)
B	KOG1802	e2gk6B3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: KOG1802	ECOD (1.6)
B	AAA_12	e2gk6B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_12	ECOD (1.6)
B	AAA_11	e2gk6B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Regulator of nonsense transcripts 1	catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein-containing complex binding chromatin binding binding RNA binding organic cyclic compound binding nucleic acid binding sequence-specific DNA binding DNA binding telomeric DNA binding adenyl ribonucleotide binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein-containing complex binding chromatin binding binding RNA binding organic cyclic compound binding nucleic acid binding sequence-specific DNA binding DNA binding telomeric 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 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 ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA double-stranded DNA helicase activity	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process organic substance biosynthetic 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic 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 cellular process regulation of metabolic process organic substance catabolic process cell cycle phase transition cell cycle cell cycle 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 organic substance transport nucleic acid transport intracellular transport establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to stimulus response to lipid 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 cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin regulation of cellular component organization organonitrogen compound biosynthetic process protein-containing complex disassembly 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 organonitrogen compound metabolic process 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 nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic 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 positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of mRNA processing RNA splicing 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 positive regulation of cellular biosynthetic process histone mRNA catabolic process histone mRNA metabolic process DNA duplex unwinding DNA geometric change DNA conformation change 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 cytokine cellular response to interleukin-1 cellular response to cytokine stimulus response to interleukin-1	intracellular anatomical structure cytoplasm cellular anatomical entity 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 intracellular anatomical structure cytoplasm cellular anatomical entity 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 protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle 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
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 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.