2EKK | pdb_00002ekk

Solution structure of RUH-074, a human UBA domain

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)
A	SCOP2 Family	UBA domain	8087315	4000749	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UBA-like	8087316	3001235	SCOP2 (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	Glyco_hydro_16, SKN1_KRE6_Sbg1	e2ekkA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: Glyco_hydro_16, SKN1_KRE6_Sbg1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22562	UBA-like domain (UBA_7)	UBA-like domain	This entry represents a UBA domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	UBA domain from E3 ubiquitin-protein ligase HUWE1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity DNA binding binding nucleic acid binding RNA binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity DNA binding binding nucleic acid binding RNA binding histone ubiquitin ligase activity histone modifying activity	regulation of cellular component organization regulation of cellular process regulation of developmental process negative regulation of mitochondrial fusion negative regulation of biological process cellular component organization negative regulation of cellular process anatomical structure development regulation of mitochondrial fusion cellular component organization or biogenesis mitochondrial fusion regulation of anatomical structure morphogenesis mitochondrion organization developmental process regulation of cellular component organization regulation of cellular process regulation of developmental process negative regulation of mitochondrial fusion negative regulation of biological process cellular component organization negative regulation of cellular process anatomical structure development regulation of mitochondrial fusion cellular component organization or biogenesis mitochondrial fusion regulation of anatomical structure morphogenesis mitochondrion organization developmental process regulation of biological process negative regulation of cellular component organization negative regulation of developmental process biological regulation regulation of organelle organization organelle fusion anatomical structure morphogenesis organelle organization negative regulation of organelle organization regulation of mitochondrion organization cellular process catabolic process regulation of type 2 mitophagy macroautophagy positive regulation of type 2 mitophagy autophagy positive regulation of biological process regulation of autophagy positive regulation of autophagy of mitochondrion positive regulation of metabolic process mitophagy regulation of autophagy of mitochondrion positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy type 2 mitophagy metabolic process regulation of metabolic process autophagy of mitochondrion regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein metabolic process protein polyubiquitination 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 protein K48-linked ubiquitination cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress DNA repair intracellular receptor signaling pathway negative regulation of signaling signaling negative regulation of intracellular signal transduction regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication regulation of intracellular signal transduction signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction peroxisome proliferator activated receptor signaling pathway regulation of response to stimulus regulation of cell communication regulation of peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway negative regulation of peroxisome proliferator activated receptor signaling pathway protein monoubiquitination membrane organization membrane fusion positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction positive regulation of response to stimulus intracellular signaling cassette positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of signaling protein branched polyubiquitination cellular developmental process cell differentiation regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process Golgi organization endomembrane system organization	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell projection cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell projection sperm principal piece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection sperm midpiece Golgi membrane Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle membrane mitochondrion sperm end piece membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleus nucleoplasm nuclear lumen vesicle lumen cytoplasmic vesicle lumen secretory granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR010309	E3 ubiquitin ligase, domain of unknown function DUF908	Domain
A	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A	IPR050409	E3 ubiquitin-protein ligase	Family
A	IPR010314	E3 ubiquitin ligase, domain of unknown function DUF913	Domain
A	IPR025527	HUWE1/REV1, ubiquitin-binding motif	Conserved Site
A	IPR004170	WWE domain	Domain
A	IPR009060	UBA-like superfamily	Homologous Superfamily
A	IPR041918	HUWE1, UBA domain	Domain
A	IPR015940	Ubiquitin-associated domain	Domain
A	IPR000569	HECT domain	Domain
A	IPR037197	WWE domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q7Z6Z7	intellectual disability, X-linked syndromic, Turner type Mental retardation, X-linked, syndromic, Turner type intellectual disability astrocytic tumor craniosynostosis malignant glioma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor chromosome Xp11.22 duplication syndrome intellectual disability, X-linked syndromic, Turner type Mental retardation, X-linked, syndromic, Turner type intellectual disability astrocytic tumor craniosynostosis malignant glioma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor chromosome Xp11.22 duplication syndrome malignant ependymoma ovarian cancer 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.