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- EMDB-53322: Structure of the MMM ubiquitin ligase complex with nanobody 270 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-53322
TitleStructure of the MMM ubiquitin ligase complex with nanobody 270 (Consensus map)
Map data
Sample
  • Complex: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
    • Complex: MOSMO
      • Protein or peptide: Human Modulator of Smoothened (MOSMO)
    • Complex: MEGF8
      • Protein or peptide: Human Multiple Epidermal Growth Factor-like Domains Protein 8 (MEGF8)
    • Complex: Nanobody 270
      • Protein or peptide: Nanobody 270
    • Complex: MGRN1
      • Protein or peptide: Human Mahogunin Ring Finger 1 (MGRN1) E3 ligase
KeywordsE3 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 information


left/right pattern formation / embryonic skeletal system development / embryonic limb morphogenesis / regulation of neuron differentiation / ciliary membrane / smoothened signaling pathway / lung development / negative regulation of smoothened signaling pathway / regulation of protein stability / RING-type E3 ubiquitin transferase ...left/right pattern formation / embryonic skeletal system development / embryonic limb morphogenesis / regulation of neuron differentiation / ciliary membrane / smoothened signaling pathway / lung development / negative regulation of smoothened signaling pathway / regulation of protein stability / RING-type E3 ubiquitin transferase / intracellular protein localization / heart development / gene expression / in utero embryonic development / cell differentiation / Golgi apparatus / plasma membrane
Similarity search - Function
Modulator of smoothened protein / Attenuator of Hedgehog
Similarity search - Domain/homology
Isoform 4 of E3 ubiquitin-protein ligase MGRN1 / Isoform 2 of Multiple epidermal growth factor-like domains protein 8 / Modulator of smoothened protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWilliams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Latorraca NR / Lartey D / Gao L ...Williams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Latorraca NR / Lartey D / Gao L / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse SL / Marqusee S / Kong JH / Rohatgi R / Siebold C
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Cancer Research UKDRCRPG-May23/100002 United Kingdom
Wellcome Trust218482/Z/19/Z United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: Mol Cell / Year: 2026
Title: Design principles of a membrane-tethered ubiquitin ligase
Authors: Williams C / Nocka LM / Hedger G / Carrique L / Pusapati GV / Parashara P / Latorraca NR / Lartey D / Gao L / Pardon E / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse SL / Marqusee S ...Authors: Williams C / Nocka LM / Hedger G / Carrique L / Pusapati GV / Parashara P / Latorraca NR / Lartey D / Gao L / Pardon E / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse SL / Marqusee S / Kong JH / Siebold C / Rohatgi R
History
DepositionApr 4, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53322.png

Downloads & links

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Map

FileDownload / File: emd_53322.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 350.544 Å		0.73 Å/pix.
x 480 pix.
= 350.544 Å		0.73 Å/pix.
x 480 pix.
= 350.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-1.4277248 - 1.7957057
Average (Standard dev.)-0.0001096793 (±0.020696726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 350.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53322_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53322_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270

EntireName: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
Components
  • Complex: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
    • Complex: MOSMO
      • Protein or peptide: Human Modulator of Smoothened (MOSMO)
    • Complex: MEGF8
      • Protein or peptide: Human Multiple Epidermal Growth Factor-like Domains Protein 8 (MEGF8)
    • Complex: Nanobody 270
      • Protein or peptide: Nanobody 270
    • Complex: MGRN1
      • Protein or peptide: Human Mahogunin Ring Finger 1 (MGRN1) E3 ligase

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Supramolecule #1: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270

SupramoleculeName: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: MMM complex was obtained by co-expression of MEGF8, MOSMO and MGRN1 components in HEK293S GnTI- TetR cells. The MMM complex was purified by tandem affinity purification. Purified nanobody ...Details: MMM complex was obtained by co-expression of MEGF8, MOSMO and MGRN1 components in HEK293S GnTI- TetR cells. The MMM complex was purified by tandem affinity purification. Purified nanobody 270, from E. coli WK6 cells, was added to MMM complex and the MMM-nanobody 270 complex formed on size-exclusion chromatography.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: MOSMO

SupramoleculeName: MOSMO / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Ternary complex with MEGF8 and MGRN1 was obtained by co-expressing MEGF8, MOSMO and MGRN1 to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: MEGF8

SupramoleculeName: MEGF8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: MEGF8 was co-expressed with MOSMO and MGRN1 to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Nanobody 270

SupramoleculeName: Nanobody 270 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Lama glama (llama)

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Supramolecule #5: MGRN1

SupramoleculeName: MGRN1 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Details: MGRN1 was co-expressed with MEGF8 and MOSMO to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Human Modulator of Smoothened (MOSMO)

MacromoleculeName: Human Modulator of Smoothened (MOSMO) / type: protein_or_peptide / ID: 1
Details: MOSMO with C-terminal 3C protease cleavage site-TwinStrep tags. Cys164 is palmitoylated (PLM).
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDKLTIISGC LFLAADIFAI ASIANPDWIN TGESAGALTV GLVRQCQTIH GRDRTCIPPR LPPEWVTTLF FIIMGIISLT VTCGLLVASH WRREATKYAR WIAFTGMILF CMAALIFPIG FYINEVGGQP YKLPNNTVVG SSYVLFVLSI FFTIVGLLFA GKVCLPGGTL ...String:
MDKLTIISGC LFLAADIFAI ASIANPDWIN TGESAGALTV GLVRQCQTIH GRDRTCIPPR LPPEWVTTLF FIIMGIISLT VTCGLLVASH WRREATKYAR WIAFTGMILF CMAALIFPIG FYINEVGGQP YKLPNNTVVG SSYVLFVLSI FFTIVGLLFA GKVCLPGGTL EVLFQGPGGS GSAWSHPQFE KGGGSGGGSG GSAWSHPQFE K

UniProtKB: Modulator of smoothened protein

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Macromolecule #2: Human Multiple Epidermal Growth Factor-like Domains Protein 8 (MEGF8)

MacromoleculeName: Human Multiple Epidermal Growth Factor-like Domains Protein 8 (MEGF8)
type: protein_or_peptide / ID: 2
Details: Human MEGF8 (residues 2312-2778) with C-terminal 1D4 epitope tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: KCQCNGHADT CNEQDGTGCP CQNNTETGTC QGSSPSDRRD CYKYQCAKCR ESFHGSPLGG QQCYRLISVE QECCLDPTSQ TNCFHEPKRR ALGPGRTVLF GVQPKFTNVD IRLTLDVTFG AVDLYVSTSY DTFVVRVAPD TGVHTVHIQP PPAPPPPPPP ADGGPRGAGD ...String:
KCQCNGHADT CNEQDGTGCP CQNNTETGTC QGSSPSDRRD CYKYQCAKCR ESFHGSPLGG QQCYRLISVE QECCLDPTSQ TNCFHEPKRR ALGPGRTVLF GVQPKFTNVD IRLTLDVTFG AVDLYVSTSY DTFVVRVAPD TGVHTVHIQP PPAPPPPPPP ADGGPRGAGD PGGAGASSGP GAPAEPRVRE VWPRGLITYV TVTEPSAVLV VRGVRDRLVI TYPHEHHALK SSRFYLLLLG VGDPSGPGAN GSADSQGLLF FRQDQAHIDL FVFFSVFFSC FFLFLSLCVL LWKAKQALDQ RQEQRRHLQE MTKMASRPFA KVTVCFPPDP TAPASAWKPA GLPPPAFRRS EPFLAPLLLT GAGGPWGPMG GGCCPPAIPA TTAGLRAGPI TLEPTEDGMA GVATLLLQLP GGPHAPNGAC LGSALVTLRH RLHEYCGGGG GAGGSGHGTG AGRKGLLSQD NLTSMSLGTE TSQVAPA

UniProtKB: Isoform 2 of Multiple epidermal growth factor-like domains protein 8

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Macromolecule #3: Nanobody 270

MacromoleculeName: Nanobody 270 / type: protein_or_peptide / ID: 3 / Details: Nanobody 270 with C-terminal His6-EPEA tag. / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGSIFS YDDMGWYRQA PGKQRELVAT FTNVGSTNYV DSVKGRFTIS RDNAKNTVYL QMNSLKPEDT AVYYCHAYTV RRFQGMEYWG KGTQVTVSSH HHHHHEPEA

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Macromolecule #4: Human Mahogunin Ring Finger 1 (MGRN1) E3 ligase

MacromoleculeName: Human Mahogunin Ring Finger 1 (MGRN1) E3 ligase / type: protein_or_peptide / ID: 4 / Details: Full-length human MGRN1 with C-terminal His-6 tag. / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGSILSRRIA GVEDIDIQAN SAYRYPPKSG NYFASHFFMG GEKFDTPHPE GYLFGENMDL NFLGSRPVQF PYVTPAPHEP VKTLRSLVN IRKDSLRLVR YKDDADSPTE DGDKPRVLYS LEFTFDADAR VAITIYCQAS EEFLNGRAVY SPKSPSLQSE T VHYKRGVS ...String:
MGSILSRRIA GVEDIDIQAN SAYRYPPKSG NYFASHFFMG GEKFDTPHPE GYLFGENMDL NFLGSRPVQF PYVTPAPHEP VKTLRSLVN IRKDSLRLVR YKDDADSPTE DGDKPRVLYS LEFTFDADAR VAITIYCQAS EEFLNGRAVY SPKSPSLQSE T VHYKRGVS QQFSLPSFKI DFSEWKDDEL NFDLDRGVFP VVIQAVVDEG DVVEVTGHAH VLLAAFEKHM DGSFSVKPLK QK QIVDRVS YLLQEIYGIE NKNNQETKPS DDENSDNSNE CVVCLSDLRD TLILPCRHLC LCTSCADTLR YQANNCPICE LPF RALLQI RAVRKKPGAL SPVSFSPVLA QSLEHDEHSN SDSVPPGYEP ISLLEALNGL RAVSPAIPSA PLYEEITYSG ISDG LSQAS CPLAAIDHIL DSSRQKGRPQ SKAPDSTLRS PSSPIHEEDE EKLSEDVDAP PPLGGAELAL RESSSPESFI TEEVD ESSS PQQGTRAASI ENVLQDSSPE HCGRGPPADI YLPALGPDSC SVGIDEGTKH HHHHH

UniProtKB: Isoform 4 of E3 ubiquitin-protein ligase MGRN1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H19NO4SHEPES
2.0 % v/vC3H8O3glycerol
2.0 mMCaCl2calcium chloride
0.02 % w/vC19H36O10glycyl-dodecyl-beta-D-maltoside (GDN)

Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 2% (v/v) glycerol, 2 mM CaCl2, 0.02% (w/v) GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
SoftwareName: EPU (ver. 3.6)
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 12956 / Average exposure time: 3.1 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in counted mode.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionNumber selected: 4203652
Details: 2D classes from a Glacios screening dataset facilitated template particle picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Patch CTF
Details: Patch CTF estimation was performed in cryoSPARC live pre-processing.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: AlphaFold2 and AlphaFold3 were used to generate a model of the MMM complex, and for nanobody 270.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-uniform refinement
Details: Non-uniform refinement of a class from 3D classification (without alignment).
Number images used: 142461
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 128000 / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: 3D classification (without alignment)
Details: 3D classification (without alignment) was performed with a mask around the transmembrane and extracellular domains of MEGF8, MOSMO and nanobody 270.

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.9)
DetailsInitial local fitting was done using ChimeraX then manual model building in Coot was interspersed with real space refinement in Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 78.5

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