9QRU | pdb_00009qru

Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 270 (Composite map)

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF18800	Attenuator of Hedgehog (Atthog)	Attenuator of Hedgehog	-	Family
A [auth D]	PF26192	RNF157-like N-terminal domain (RNF157-like_N)	RNF157-like N-terminal domain	This entry describes the N-terminal domain in E3 ubiquitin ligases, including MGNR1, LUL1-4, RNF157 and LOG2. E3 ubiquitin ligase proteins are involved in the ubiquitination process, where ubiquitin is transferred to substrate proteins, marking them ...	This entry describes the N-terminal domain in E3 ubiquitin ligases, including MGNR1, LUL1-4, RNF157 and LOG2. E3 ubiquitin ligase proteins are involved in the ubiquitination process, where ubiquitin is transferred to substrate proteins, marking them for degradation or altering their cellular functions. MGRN1 is involved in endosome-to-lysosome trafficking and negatively regulates signalling pathways like hedgehog signalling. RNF157 is crucial for neuronal survival and dendrite maintenance, acting as a scaffold in signalling pathways that regulate the cell cycle. LOG2 and its subfamily members, including LUL proteins, are involved in amino acid homeostasis and secretion [4-6]. This domain is usually found N-terminal to the C3HC4 zinc finger (Pfam:PF13920). In human RNF157 (Swiss:Q96PX1), the N-terminal domain binds to the second PTB domain of Fe65 [7]. This domain is predicted to have an Ig-like fold.	Domain
A [auth D]	PF13920	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_3)	Zinc finger, C3HC4 type (RING finger)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B]	Isoform 2 of Multiple epidermal growth factor-like domains protein 8	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding	developmental process multicellular organismal process embryonic morphogenesis embryo development gastrulation multicellular organism development anatomical structure morphogenesis ameboidal-type cell migration anatomical structure development cell migration cellular process cell motility cell migration involved in gastrulation animal gross anatomical part developmental process developmental process multicellular organismal process embryonic morphogenesis embryo development gastrulation multicellular organism development anatomical structure morphogenesis ameboidal-type cell migration anatomical structure development cell migration cellular process cell motility cell migration involved in gastrulation animal gross anatomical part developmental process cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway heart development epithelium development embryonic heart tube left/right pattern formation tube development animal organ development pattern specification process tissue development embryonic heart tube development regionalization circulatory system development embryonic organ development left/right pattern formation system development determination of heart left/right asymmetry determination of bilateral symmetry determination of left/right symmetry specification of symmetry axon extension positive regulation of nervous system development positive regulation of locomotion regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development positive regulation of chemotaxis regulation of cell development positive regulation of axon extension involved in axon guidance positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis taxis cell differentiation positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth chemotaxis regulation of cell projection organization positive regulation of cell development response to external stimulus nervous system development developmental growth involved in morphogenesis generation of neurons regulation of response to stimulus response to chemical regulation of locomotion positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell growth cell morphogenesis regulation of axon extension cellular component organization regulation of nervous system development positive regulation of response to stimulus neurogenesis regulation of axon extension involved in axon guidance regulation of extent of cell growth positive regulation of response to external stimulus positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis axon extension involved in axon guidance positive regulation of axon extension positive regulation of cellular process positive regulation of axonogenesis regulation of anatomical structure morphogenesis locomotion regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth axon guidance positive regulation of cell growth axon development regulation of chemotaxis regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth neuron projection guidance neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process embryonic organ morphogenesis chordate embryonic development embryo development ending in birth or egg hatching skeletal system development animal organ morphogenesis embryonic skeletal system development skeletal system morphogenesis embryonic skeletal system morphogenesis epiboly involved in gastrulation with mouth forming second morphogenesis of an epithelium morphogenesis of an epithelial sheet tissue morphogenesis gastrulation with mouth forming second epiboly negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process regulation of smoothened signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of cell communication limb development appendage development embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis digestive system development digestive tract development determination of digestive tract left/right asymmetry heart morphogenesis tube morphogenesis embryonic heart tube morphogenesis epithelial tube morphogenesis craniofacial suture morphogenesis cranial skeletal system development bone morphogenesis bone development neuron recognition neuron projection fasciculation axonal fasciculation cell recognition fasciculation of sensory neuron axon	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex ubiquitin ligase complex catalytic complex transferase complex cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular organelle intracellular anatomical structure nucleus intracellular membrane-bounded organelle
D [auth C]	Nanobody 270	-	-	-
B [auth A]	Modulator of smoothened protein	-	regulation of protein stability biological regulation regulation of biological quality developmental process cellular developmental process cell differentiation cellular process multicellular organismal process regulation of biological process regulation of cellular process regulation of developmental process regulation of cell differentiation nervous system development generation of neurons regulation of protein stability biological regulation regulation of biological quality developmental process cellular developmental process cell differentiation cellular process multicellular organismal process regulation of biological process regulation of cellular process regulation of developmental process regulation of cell differentiation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation anatomical structure development animal gross anatomical part developmental process regulation of neuron differentiation system development cellular response to stimulus response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cilium ciliary membrane cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cilium ciliary membrane plasma membrane bounded cell projection cell projection bounding membrane of organelle plasma membrane region organelle membrane cell projection membrane
A [auth D]	Isoform 4 of E3 ubiquitin-protein ligase MGRN1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity molecular sequestering activity protein sequestering 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 transferase activity catalytic activity ubiquitin-protein transferase activity molecular sequestering activity protein sequestering activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation smoothened signaling pathway cell communication cellular process signal transduction cellular localization transport endosome to lysosome transport cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation smoothened signaling pathway cell communication cellular process signal transduction cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell vacuolar transport negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication negative regulation of cellular process regulation of G protein-coupled receptor signaling pathway regulation of signaling negative regulation of response to stimulus adenylate cyclase-activating G protein-coupled receptor signaling pathway negative regulation of signal transduction negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of response to stimulus adenylate cyclase-modulating G protein-coupled receptor signaling pathway regulation of cell communication G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway primary metabolic process protein monoubiquitination 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 pigment metabolic process regulation of melanin biosynthetic process pigment biosynthetic process negative regulation of secondary metabolite biosynthetic process melanin metabolic process secondary metabolic process secondary metabolite biosynthetic process regulation of biosynthetic process negative regulation of metabolic process regulation of secondary metabolite biosynthetic process regulation of secondary metabolic process biosynthetic process negative regulation of biosynthetic process negative regulation of melanin biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process melanin biosynthetic process regulation of metabolic process negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway response to nutrient levels regulation of response to nutrient levels positive regulation of appetite positive regulation of biological process positive regulation of response to stimulus regulation of response to food response to food response to chemical regulation of biological quality positive regulation of response to food regulation of appetite positive regulation of response to nutrient levels	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle membrane membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol cell periphery plasma membrane protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B]	IPR024731	NELL2-like, EGF domain	Domain
C [auth B]	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
C [auth B]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C [auth B]	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
C [auth B]	IPR016201	PSI domain	Domain
C [auth B]	IPR002049	Laminin-type EGF domain	Domain
C [auth B]	IPR000859	CUB domain	Domain
C [auth B]	IPR000742	EGF-like domain	Domain
C [auth B]	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
C [auth B]	IPR002165	Plexin repeat	Repeat
C [auth B]	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
C [auth B]	IPR056737	Attractin/MKLN-like, beta-propeller domain	Domain
C [auth B]	IPR001881	EGF-like calcium-binding domain	Domain
C [auth B]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
B [auth A]	IPR037663	Modulator of smoothened protein	Family
A [auth D]	IPR058981	MGRN1/RNF157-like, N-terminal domain	Domain
A [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth D]	IPR001841	Zinc finger, RING-type	Domain
A [auth D]	IPR045194	E3 ubiquitin-protein ligase MGRN1/RNF157-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth B]	: Q7Z7M0	Carpenter syndrome craniosynostosis MEGF8-related Carpenter syndrome acrocephalosyndactyly large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma lung cancer intellectual disability malignant glioma polydactyly
B [auth A]	: Q8NHV5	atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma ovarian cancer subependymal giant cell astrocytoma gastric cancer hepatocellular carcinoma malignant glioma pilocytic astrocytoma tuberculosis gastric carcinoma large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor
A [auth D]	: O60291	astrocytic tumor ovarian cancer breast carcinoma psoriasis osteosarcoma

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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.