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	UBA	e2ekkA1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA	ECOD (1.6)

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 RNA binding binding nucleic acid binding DNA 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 RNA binding binding nucleic acid binding DNA binding histone ubiquitin ligase activity histone modifying activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling protein polyubiquitination protein branched polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal developmental process cellular developmental process cell differentiation regulation of cellular component organization regulation of developmental process negative regulation of mitochondrial fusion negative regulation of biological process negative regulation of cellular process anatomical structure development regulation of mitochondrial fusion mitochondrial fusion regulation of anatomical structure morphogenesis mitochondrion organization negative regulation of cellular component organization negative regulation of developmental process regulation of organelle organization organelle fusion anatomical structure morphogenesis organelle organization negative regulation of organelle organization regulation of mitochondrion organization 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 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 regulation of macromolecule metabolic process regulation of metabolic process catabolic process regulation of type 2 mitophagy macroautophagy positive regulation of type 2 mitophagy autophagy regulation of autophagy positive regulation of autophagy of mitochondrion mitophagy regulation of autophagy of mitochondrion positive regulation of macroautophagy process utilizing autophagic mechanism 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 autophagy of mitochondrion proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of localization establishment of protein localization regulation of protein localization protein targeting regulation of protein targeting to mitochondrion regulation of establishment of protein localization positive regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion localization establishment of protein localization to organelle regulation of protein targeting macromolecule localization protein targeting to mitochondrion positive regulation of protein targeting to mitochondrion intracellular protein localization establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion protein K48-linked ubiquitination 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 negative regulation of intracellular signal transduction negative regulation of cell communication negative regulation of response to stimulus negative regulation of signal transduction peroxisome proliferator activated receptor signaling pathway regulation of peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway negative regulation of peroxisome proliferator activated receptor signaling pathway protein monoubiquitination Golgi organization endomembrane system organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule endomembrane system intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleus nucleoplasm nuclear lumen Golgi membrane Golgi apparatus bounding membrane of organelle organelle membrane 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	IPR041918	HUWE1, UBA domain	Domain
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	IPR015940	Ubiquitin-associated domain	Domain
A	IPR000569	HECT domain	Domain
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	IPR037197	WWE domain superfamily	Homologous Superfamily
A	IPR009060	UBA-like 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.