3VHT

Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin

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	d3vhta1	Alpha and beta proteins (a+b)	GFP-like	GFP-like	Fluorescent proteins	Green fluorescent protein, GFP	Jellyfish (Aequorea victoria ) [TaxId: 6100 ],	SCOPe (2.08)
A	d3vhta2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Jellyfish (Aequorea victoria ) [TaxId: 6100 ],	SCOPe (2.08)
C	d3vhtc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GFP-like	8096046	3000576	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GFP-like	8096046	3000576	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8098882	3000157	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	GFP	e3vhtA1	A: beta barrels	X: GFP-like (From Topology)	H: GFP-like (From Topology)	T: GFP-like	F: GFP	ECOD (1.6)
B	GFP	e3vhtB1	A: beta barrels	X: GFP-like (From Topology)	H: GFP-like (From Topology)	T: GFP-like	F: GFP	ECOD (1.6)
B	Sgf11_2	e3vhtB2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: Sgf11_2	ECOD (1.6)
C	ubiquitin_1	e3vhtC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.155.10	Mainly Beta	Beta Barrel	Green Fluorescent Protein	Green fluorescent protein	CATH (4.3.0)
B	2.40.155.10	Mainly Beta	Beta Barrel	Green Fluorescent Protein	Green fluorescent protein	CATH (4.3.0)
B	3.30.160.60	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Classic Zinc Finger	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01353	Green fluorescent protein (GFP)	Green fluorescent protein	-	Domain
B	PF18279	Werner helicase-interacting protein 1 ubiquitin-binding domain (zf-WRNIP1_ubi)	Werner helicase-interacting protein 1 ubiquitin-binding domain	This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ [1].	Domain
B	PF01353	Green fluorescent protein (GFP)	Green fluorescent protein	-	Domain
C	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Green fluorescent protein	-	bioluminescence cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	-
B	Green fluorescent protein,ATPase WRNIP1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity 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 ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid single-stranded DNA helicase activity helicase activity cation binding metal ion binding identical protein binding protein binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA-templated DNA replication DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA-templated DNA replication DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus cellular response to stimulus cellular biosynthetic process DNA synthesis involved in DNA repair nucleic acid biosynthetic process cellular response to stress organic substance biosynthetic process DNA repair cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process DNA damage response organic cyclic compound biosynthetic process cellular process DNA biosynthetic process regulation of DNA-templated DNA replication initiation regulation of biological process DNA replication initiation biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process bioluminescence generation of precursor metabolites and energy	membrane cellular anatomical entity intracellular anatomical structure perinuclear region of cytoplasm cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C	Ubiquitin	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding metal ion binding small molecule binding	organonitrogen compound metabolic process translation at synapse cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation at presynapse translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process organonitrogen compound metabolic process translation at synapse cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation at presynapse translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis organic substance catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cytoplasmic translation cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis ribosomal small subunit biogenesis translation at postsynapse	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle myelin sheath cytoplasm cytosol presynapse synapse cell junction nucleoplasm ribosome cytosolic ribosome preribosome protein-containing complex ribonucleoprotein complex small-subunit processome cytosolic small ribosomal subunit small ribosomal subunit ribosomal subunit postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000786	Green fluorescent protein, GFP	Family
A	IPR011584	Green fluorescent protein-related	Family
A	IPR009017	Green fluorescent protein	Homologous Superfamily
B	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
B	IPR040539	WRNIP1, ubiquitin-binding domain	Domain
B	IPR003593	AAA+ ATPase domain	Domain
B	IPR021886	MgsA AAA+ ATPase C-terminal	Domain
B	IPR003959	ATPase, AAA-type, core	Domain
B	IPR006642	Rad18, zinc finger UBZ4-type	Domain
B	IPR032423	AAA C-terminal domain	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR000786	Green fluorescent protein, GFP	Family
B	IPR011584	Green fluorescent protein-related	Family
B	IPR009017	Green fluorescent protein	Homologous Superfamily
C	IPR019954	Ubiquitin conserved site	Conserved Site
C	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
C	IPR000626	Ubiquitin-like domain	Domain
C	IPR038582	Small ribosomal subunit protein eS31 eukaryotic-type superfamily	Homologous Superfamily
C	IPR002906	Small ribosomal subunit protein eS31	Domain
C	IPR019956	Ubiquitin domain	Domain
C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily