4XI6 | pdb_00004xi6

Crystal structure of the MZM-REP domains of Mind bomb 1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	MIB_REP	e4xi6A4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MIB_REP	ECOD (1.6)
A	MIB_HERC2	e4xi6A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MIB_HERC2	ECOD (1.6)
A	ZZ	e4xi6A2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: ZZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00569	Zinc finger, ZZ type (ZZ)	Zinc finger, ZZ type	Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure [2].	Domain
A	PF18346	Mind bomb SH3 repeat domain (SH3_15)	Mind bomb SH3 repeat domain	The REP domain of Mind bomb which serves as the substrate recognition domain for a second, membrane-distal epitope of the Notch ligand (C-box). Although the first Mib repeat of REP may play a dominant role in ligand binding, the two repeats appear t ...	The REP domain of Mind bomb which serves as the substrate recognition domain for a second, membrane-distal epitope of the Notch ligand (C-box). Although the first Mib repeat of REP may play a dominant role in ligand binding, the two repeats appear to cooperate in the engagement of the Jag1 tail. Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. The structure and functional analysis, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membrane proximal region and the other near the C terminus. REP domains have a five-stranded anti-parallel twisted beta sheet topology similar to that of SH3 domains [1].	Domain
A	PF06701	Mib_herc2 (MIB_HERC2)	Mib_herc2	Named "mib/herc2 domain" in [1]. Usually the protein also contains an E3 ligase domain (either Ring or Hect).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	E3 ubiquitin-protein ligase MIB1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation somitogenesis epithelium development chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo development tissue development regionalization anatomical structure morphogenesis embryo development ending in birth or egg hatching somite development anatomical structure formation involved in morphogenesis localization import into cell transport endocytosis establishment of localization vesicle-mediated transport central nervous system neuron differentiation central nervous system development 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 embryonic epithelial tube formation tube formation epithelial tube formation tube morphogenesis epithelial tube morphogenesis morphogenesis of embryonic epithelium neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue morphogenesis neural tube formation in utero embryonic development 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 ubiquitin-dependent protein catabolic process vasculature development blood vessel development circulatory system development cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication Notch signaling pathway signal transduction regulation of localization positive regulation of cellular component organization regulation of cellular component organization regulation of transport positive regulation of biological process regulation of vesicle-mediated transport cellular component organization positive regulation of endocytosis positive regulation of transport cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis heart morphogenesis embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of bilateral symmetry animal organ morphogenesis embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis heart development animal organ development determination of heart left/right asymmetry left/right pattern formation	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton centriolar satellite cytoplasm cytosol cell periphery intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton centriolar satellite cytoplasm cytosol cell periphery plasma membrane membrane synapse cell junction glutamatergic synapse membrane-bounded organelle cytoplasmic vesicle intracellular vesicle intracellular membrane-bounded organelle vesicle postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR040847	Mind bomb, SH3 repeat domain	Domain
A	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR010606	Mib-herc2	Domain
A	IPR000433	Zinc finger, ZZ-type	Domain
A	IPR002110	Ankyrin repeat	Repeat
A	IPR037252	Mib/herc2 domain superfamily	Homologous Superfamily
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR042056	E3 ubiquitin-protein ligase MIB1/2, zinc finger, ZZ-type	Domain
A	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q86YT6	left ventricular noncompaction left ventricular noncompaction 7 visual epilepsy Gustatory seizure malignant pancreatic neoplasm myopathy ovarian cancer Crohn disease rheumatoid arthritis gastric cancer hepatocellular carcinoma juvenile dermatomyositis medulloblastoma acute myeloid leukemia atypical teratoid rhabdoid tumor left ventricular noncompaction left ventricular noncompaction 7 visual epilepsy Gustatory seizure malignant pancreatic neoplasm myopathy ovarian cancer Crohn disease rheumatoid arthritis gastric cancer hepatocellular carcinoma juvenile dermatomyositis medulloblastoma acute myeloid leukemia atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma diabetes mellitus gastric carcinoma glioblastoma intellectual disability large cell medulloblastoma malignant ependymoma non-small cell lung carcinoma amyotrophic lateral sclerosis cardiomyopathy osteosarcoma Pick disease Emery-Dreifuss muscular dystrophy exocrine pancreatic carcinoma

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.