4PYU | pdb_00004pyu

The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells

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)
K [auth S]	SCOP2B Superfamily	Ubiquitin-like	8038047	3000157	SCOP2B (2022-06-29)
I [auth O]	SCOP2B Superfamily	Ubiquitin-like	8038047	3000157	SCOP2B (2022-06-29)
G [auth K]	SCOP2B Superfamily	Ubiquitin-like	8038047	3000157	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	Ubiquitin-like	8038047	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8038047	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8038047	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)
K [auth S]		e4pyuS1	A: alpha/beta-Hydrolases	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: RVP	F:	ECOD (20:10:01)
I [auth O]		e4pyuO1	A: alpha/beta-Hydrolases	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: RVP	F:	ECOD (20:10:01)
G [auth K]		e4pyuK1	A: alpha/beta-Hydrolases	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: RVP	F:	ECOD (20:10:01)
E [auth G]		e4pyuG1	A: alpha/beta-Hydrolases	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: RVP	F:	ECOD (20:10:01)
B		e4pyuB1	A: alpha/beta-Hydrolases	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: RVP	F:	ECOD (20:10:01)
A		e4pyuA1	A: alpha/beta-Hydrolases	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: RVP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K [auth S]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
I [auth O]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G [auth K]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E [auth G]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	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
C, D, F [auth H], H [auth L], J [auth P], C, D, F [auth H], H [auth L], J [auth P], L [auth T]	PF19252	HIND motif (HIND)	HIND motif	-	Motif
A, B, E [auth G], G [auth K], I [auth O], A, B, E [auth G], G [auth K], I [auth O], K [auth S]	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
C, D, F [auth H], H [auth L], J [auth P], C, D, F [auth H], H [auth L], J [auth P], L [auth T]	U4/U6.U5 tri-snRNP-associated protein 1	RNA binding binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process maturation of 5S rRNA RNA splicing mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile multicellular organismal process regulation of leukocyte differentiation regulation of cellular process regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell activation T cell activation cell differentiation anatomical structure development positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process developmental process regulation of biological process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process leukocyte differentiation cellular developmental process regulation of developmental process positive regulation of biological process cell development positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion regulation of cytotoxic T cell differentiation cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process regulation of lymphocyte differentiation regulation of multicellular organismal development cytotoxic T cell differentiation hemopoiesis positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation immune system process regulation of hemopoiesis positive regulation of cytotoxic T cell differentiation positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation protein-RNA complex assembly cellular component organization protein-RNA complex organization cellular component assembly protein-containing complex assembly protein-containing complex organization spliceosomal snRNP assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen Cajal body catalytic step 2 spliceosome protein-containing complex catalytic complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex U2-type spliceosomal complex U2-type precatalytic spliceosome precatalytic spliceosome cytosol spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex
A, B, E [auth G], G [auth K], I [auth O], A, B, E [auth G], G [auth K], I [auth O], K [auth S]	Ubiquitin-like protein 5	protein tag activity molecular tag activity	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing	membrane-bounded organelle Cajal body intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle Cajal body intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, F [auth H], H [auth L], J [auth P], C, D, F [auth H], H [auth L], J [auth P], L [auth T]	IPR045347	HIND motif	Conserved Site
C, D, F [auth H], H [auth L], J [auth P], C, D, F [auth H], H [auth L], J [auth P], L [auth T]	IPR005011	SNU66/SART1 family	Family
A, B, E [auth G], G [auth K], I [auth O], A, B, E [auth G], G [auth K], I [auth O], K [auth S]	IPR039732	Ubiquitin-like modifier Hub1/Ubl5	Family
A, B, E [auth G], G [auth K], I [auth O], A, B, E [auth G], G [auth K], I [auth O], K [auth S]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, E [auth G], G [auth K], I [auth O], A, B, E [auth G], G [auth K], I [auth O], K [auth S]	IPR000626	Ubiquitin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D, F [auth H], H [auth L], J [auth P], C, D, F [auth H], H [auth L], J [auth P], L [auth T]	Pharos: O43290	acute myeloid leukemia Crohn disease inflammatory bowel disease ovarian cancer Sjogren syndrome astrocytic tumor diabetes mellitus malignant mesothelioma plasma cell myeloma skin basal cell carcinoma congestive heart failure glioblastoma osteosarcoma primary cutaneous T-cell non-Hodgkin lymphoma
A, B, E [auth G], G [auth K], I [auth O], A, B, E [auth G], G [auth K], I [auth O], K [auth S]	Pharos: Q9BZL1	plasma cell myeloma 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.