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Yorodumi- EMDB-53340: Cryo-EM structure of the MMM ubiquitin ligase complex with nanobo... -
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Basic information
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| Title | Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map) | ||||||||||||||||||
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Keywords | E3 Ubiquitin Ligase / Hedgehog Signaling / Single-pass Membrane Protein / Membrane Protein Complex / Smoothened / Tetraspanin / Cell Surface Receptor / Primary Cilium / Morphogen / Signal Transduction / Human / Carpenter Syndrome / Cancer / Nanobody / Palmitoylation / GDN / MEMBRANE PROTEIN | ||||||||||||||||||
| Function / homology | Function and homology informationepiboly involved in gastrulation with mouth forming second / negative regulation of melanin biosynthetic process / determination of heart left/right asymmetry / determination of digestive tract left/right asymmetry / craniofacial suture morphogenesis / embryonic heart tube left/right pattern formation / left/right pattern formation / fasciculation of sensory neuron axon / cell migration involved in gastrulation / pharyngeal arch artery morphogenesis ...epiboly involved in gastrulation with mouth forming second / negative regulation of melanin biosynthetic process / determination of heart left/right asymmetry / determination of digestive tract left/right asymmetry / craniofacial suture morphogenesis / embryonic heart tube left/right pattern formation / left/right pattern formation / fasciculation of sensory neuron axon / cell migration involved in gastrulation / pharyngeal arch artery morphogenesis / positive regulation of eating behavior / embryonic skeletal system morphogenesis / embryonic skeletal system development / positive regulation of axon extension involved in axon guidance / limb morphogenesis / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / embryonic heart tube morphogenesis / embryonic brain development / coronary vasculature development / embryonic limb morphogenesis / regulation of neuron differentiation / embryonic digit morphogenesis / negative regulation of G protein-coupled receptor signaling pathway / aorta development / smoothened signaling pathway / ciliary membrane / endosome to lysosome transport / BMP signaling pathway / protein monoubiquitination / ubiquitin ligase complex / lung development / negative regulation of smoothened signaling pathway / protein sequestering activity / regulation of protein stability / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / intracellular protein localization / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heart development / regulation of gene expression / protein-containing complex assembly / gene expression / in utero embryonic development / early endosome / cell differentiation / protein ubiquitination / calcium ion binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / zinc ion binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
| Biological species | Homo sapiens (human) / ![]() | ||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Williams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Sarkar P / Latorraca NR / Lartey D ...Williams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Sarkar P / Latorraca NR / Lartey D / Gao L / Milenkovic L / Steyaert J / Bazan F / Rouse SL / Marqusee S / Kong JH / Rohatgi R / Siebold C | ||||||||||||||||||
| Funding support | United Kingdom, 5 items
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Citation | Journal: Mol Cell / Year: 2026Title: Design principles of a membrane-spanning ubiquitin ligase. Authors: Carys Williams / Laura M Nocka / George Hedger / Pragya Parashara / Els Pardon / Naomi R Latorraca / Ganesh V Pusapati / Parijat Sarkar / Dorothy Lartey / Lei Gao / Ljiljana Milenkovic / Rod ...Authors: Carys Williams / Laura M Nocka / George Hedger / Pragya Parashara / Els Pardon / Naomi R Latorraca / Ganesh V Pusapati / Parijat Sarkar / Dorothy Lartey / Lei Gao / Ljiljana Milenkovic / Rod Chalk / Jan Steyaert / Susan Marqusee / Loïc Carrique / J Fernando Bazan / Sarah L Rouse / Jennifer H Kong / Christian Siebold / Rajat Rohatgi / ![]() Abstract: Receptor-type E3 ubiquitin ligases enable extracellular signals to control ubiquitylation in the cytoplasm, playing widespread roles in development, metabolism, and immunity. Using cryoelectron ...Receptor-type E3 ubiquitin ligases enable extracellular signals to control ubiquitylation in the cytoplasm, playing widespread roles in development, metabolism, and immunity. Using cryoelectron microscopy, integrated with biophysical and functional studies, we visualized a human E3 complex composed of two transmembrane proteins, MEGF8 and MOSMO, and the intracellular RING-family protein MGRN1. This MEGF8-MOSMO-MGRN1 (MMM) complex attenuates Hedgehog signaling by ubiquitylating Smoothened (SMO), a G-protein-coupled receptor (GPCR) that transduces morphogen signals. A long helix in the MMM complex engages SMO using an intramembrane degron and extends into the cytoplasm to suspend an activated and precisely oriented RING domain below the plasma membrane. This architecture enables ubiquitylation of the cytoplasmic surface of SMO, reducing SMO abundance at primary cilia. Our structure provides insights into MEGF8 mutations, which cause multi-organ birth defects, and defines a paradigm for how transmembrane E3 ligases control the cell surface abundance of GPCRs and other signaling receptors. | ||||||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_53340.map.gz | 381.4 MB | EMDB map data format | |
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| Header (meta data) | emd-53340-v30.xml emd-53340.xml | 33.9 KB 33.9 KB | Display Display | EMDB header |
| Images | emd_53340.png | 45.2 KB | ||
| Filedesc metadata | emd-53340.cif.gz | 9.6 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-53340 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-53340 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9qshMC ![]() 9qqsC ![]() 9qruC ![]() 9qs6C ![]() 9qtyC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_53340.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.7303 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992
+Supramolecule #1: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992
+Supramolecule #2: MOSMO
+Supramolecule #3: MEGF8
+Supramolecule #4: Nanobody 992
+Supramolecule #5: MGRN1
+Macromolecule #1: Isoform 4 of E3 ubiquitin-protein ligase MGRN1
+Macromolecule #2: Modulator of smoothened protein
+Macromolecule #3: Isoform 2 of Multiple epidermal growth factor-like domains protein 8
+Macromolecule #4: Nanobody 992
+Macromolecule #5: ZINC ION
+Macromolecule #6: PALMITIC ACID
+Macromolecule #7: (1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},1...
+Macromolecule #8: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 5 mg/mL | ||||||||||||||||||
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| Buffer | pH: 7.5 Component:
Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 2% (v/v) glycerol, 2 mM CaCl2, 0.02% (w/v) GDN | ||||||||||||||||||
| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 11391 / Average exposure time: 3.1 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in counted mode. |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 165000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Initial model |
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| Details | Initial local fitting was done using ChimeraX then manual model building in Coot was interspersed with real space refinement in Phenix. | |||||||||
| Refinement | Space: REAL / Protocol: RIGID BODY FIT | |||||||||
| Output model | ![]() PDB-9qsh: |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United Kingdom, 5 items
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FIELD EMISSION GUN
