2YMB | pdb_00002ymb

Structures of MITD1

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)
D	SCOP2B Superfamily	MIT domain	8067094	3001898	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phospholipase D/nuclease-like	8092078	3000664	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phospholipase D/nuclease-like	8092078	3000664	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MIT domain	8067094	3001898	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8092078	3000664	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8092078	3000664	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)
D		e2ymbD1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Histone	F:	ECOD (20:10:01)
C		e2ymbC1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: LYTB	F:	ECOD (20:10:01)
B		e2ymbB1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Histone	F:	ECOD (20:10:01)
A		e2ymbA1	A: Ribosomal protein L31e-like	X: Reductive activator for corrinoid/iron-sulfur protein second domain	H: Reductive activator for corrinoid/iron-sulfur protein second domain	T: RACo_linker	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.58.80	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
D	3.30.870.30	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
C	1.20.58.80	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	3.30.870.30	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
B	3.30.870.30	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
A	3.30.870.30	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16565	Phospholipase D-like domain at C-terminus of MIT (MIT_C)	Phospholipase D-like domain at C-terminus of MIT	MIT_C is the C-terminal domain of MIT-containing proteins, Pfam:PF04212. It contains an unanticipated phospholipase d fold (PLD fold) that binds avidly to phosphoinositide-containing membranes [1]. It is conserved in eukaryotes, though not fungi and ...	MIT_C is the C-terminal domain of MIT-containing proteins, Pfam:PF04212. It contains an unanticipated phospholipase d fold (PLD fold) that binds avidly to phosphoinositide-containing membranes [1]. It is conserved in eukaryotes, though not fungi and plants, and some bacteria.	Domain
A, B, C, D	PF04212	MIT (microtubule interacting and transport) domain (MIT)	MIT (microtubule interacting and transport) domain	The MIT domain forms an asymmetric three-helix bundle [3] and binds ESCRT-III (endosomal sorting complexes required for transport) substrates [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	MIT DOMAIN-CONTAINING PROTEIN 1	binding phospholipid binding lipid binding phosphatidylinositol binding protein binding protein domain specific binding identical protein binding	mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function membrane organization mitotic cytokinetic process cellular component organization midbody abscission cytokinetic process cellular component organization or biogenesis	midbody cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle endosome membrane intracellular anatomical structure midbody cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome cytoplasm organelle membrane
E [auth F], F [auth H]	CHARGED MULTIVESICULAR BODY PROTEIN 1A	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity identical protein binding protein binding binding protein domain specific binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity identical protein binding protein binding binding protein domain specific binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane organization membrane biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane organization membrane biogenesis nuclear membrane reassembly membrane assembly nuclear membrane organization cellular component biogenesis nucleus organization organelle organization cellular component assembly nuclear envelope organization endomembrane system organization cell division primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process mitotic nuclear division mitotic metaphase chromosome alignment organelle fission chromosome organization sister chromatid segregation mitotic cell cycle metaphase chromosome alignment localization nuclear division mitotic cell cycle process chromosome localization organelle localization nuclear chromosome segregation mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization regulation of mitotic spindle organization membraneless organelle assembly regulation of mitotic spindle assembly regulation of cell cycle microtubule cytoskeleton organization involved in mitosis spindle organization regulation of biological process organelle assembly regulation of cell cycle process biological regulation regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization mitotic spindle organization regulation of spindle assembly mitotic spindle assembly regulation of organelle assembly microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization mitotic chromosome condensation chromosome condensation microtubule organizing center organization regulation of centrosome cycle centrosome duplication centrosome cycle regulation of centrosome duplication cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport multivesicular body sorting pathway establishment of localization in cell endosome transport via multivesicular body sorting pathway virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle ESCRT III complex disassembly ESCRT complex disassembly late endosome to vacuole transport vacuolar transport membrane fusion organelle membrane fusion endosome to lysosome transport lysosomal transport multivesicular body-lysosome fusion vesicle organization endosome to lysosome transport via multivesicular body sorting pathway lysosome organization vacuole organization lytic vacuole organization lysosomal membrane organization organelle fusion vesicle fusion multivesicular body assembly multivesicular body organization endosome organization establishment of protein localization protein transport macromolecule localization intracellular protein localization cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis cytokinesis midbody abscission cytokinetic process membrane fission biological process involved in interspecies interaction between organisms non-lytic viral release biological process involved in interaction with host biological process involved in symbiotic interaction exit from host cell viral budding from plasma membrane viral release from host cell late endosome to lysosome transport regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of macromolecule metabolic process wound healing response to stimulus plasma membrane repair response to stress plasma membrane organization response to wounding vesicle fusion with vacuole vacuole fusion	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol endosome membrane extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol endosome membrane protein-containing complex ESCRT complex endosome membrane intracellular vesicle membrane protein complex intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane ESCRT III complex organelle membrane vacuolar membrane autophagosome membrane vacuole autophagosome amphisome membrane amphisome nucleus nuclear protein-containing complex organelle envelope nuclear envelope nuclear pore lytic vacuole lytic vacuole membrane lysosomal membrane lysosome midbody membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix multivesicular body membrane late endosome membrane late endosome multivesicular body condensed nuclear chromosome intracellular membraneless organelle nuclear chromosome chromosome membraneless organelle condensed chromosome cell periphery plasma membrane early endosome polymeric cytoskeletal fiber spindle spindle microtubule kinetochore microtubule cytoskeleton supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region microtubule organizing center

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007330	MIT domain	Domain
A, B, C, D	IPR032341	MITD1, C-terminal phospholipase D-like domain	Domain
A, B, C, D	IPR036181	MIT domain superfamily	Homologous Superfamily
A, B, C, D	IPR038113	MITD1, C-terminal phospholipase D-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR045331	MITD1, N-terminal domain	Domain
A, B, C, D	IPR052817	MIT domain-containing protein 1	Family
E [auth F], F [auth H]	IPR005024	Snf7 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q8WV92	adenoma myopathy progressive supranuclear palsy juvenile dermatomyositis ovarian cancer Sjogren syndrome medulloblastoma pancreatic intraductal papillary-mucinous neoplasm
E [auth F], F [auth H]	Pharos: Q9HD42	pontocerebellar hypoplasia type 8 pontocerebellar hypoplasia Ataxias, Hereditary intellectual disability osteosarcoma squamous cell carcinoma melanoma photosensitivity disease psoriasis vitiligo cutaneous melanoma neurodegenerative disease skin basal cell 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.