Focused refinement of the MGRN1 ubiquitin ligase in complex with MEGF8, MOSMO and nanobody 992

2026-06-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-04-04 2026-05-27 2026-05-27 2026-06-17 Cancer Research UK DRCRPG-May23/100002 United Kingdom Cancer Research UK C20724/A26752 United Kingdom Wellcome Trust 218482/Z/19/Z United Kingdom Wellcome Trust 060208/Z/00/Z United Kingdom Wellcome Trust 093305/Z/10/Z United Kingdom Focused refinement of the MGRN1 ubiquitin ligase in complex with MEGF8, MOSMO and nanobody 992 Williams C Carrique L Pardon E Nocka LM Hedger G Pusapati GV Parashara P Latorraca NR Sarkar P Lartey D Gao L Milenkovic L Chalk R Steyaert J Bazan F Rouse SL Marqusee S Kong JH Rohatgi R Siebold C 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 Williams C Nocka LM Hedger G Parashara P Pardon E Latorraca NR Pusapati GV Sarkar P Lartey D Gao L Milenkovic L Chalk R Steyaert J Marqusee S Carrique L Bazan JF Rouse SL Kong JH Siebold C Rohatgi R Design principles of a membrane-spanning ubiquitin ligase. Mol.Cell US 86 2207 2222.e16 2026 42190653 doi:10.1016/j.molcel.2026.05.001 1097-2765 2168 MOCEFL EMD-53336 other EM volume

EMD-53336 contains a focused refinement of the binary MEGF8-MOSMO complex with nanobody 992.

EMD-53337 other EM volume

EMD-53336 contains a focused refinement of extracellular regions of the binary MEGF8-MOSMO complex with nanobody 992.

EMDB EMD-53336 other EM volume

EMD-53336 contains a focused refinement of the binary MEGF8-MOSMO complex with nanobody 992.

EMDB EMD-53337 other EM volume

EMD-53336 contains a focused refinement of extracellular regions of the binary MEGF8-MOSMO complex with nanobody 992.

EMDB EMD-53338 associated EM volume Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992 Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992 0 1 2 3

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 992, from E. coli WK6 cells, was added to MMM complex and the MMM-nanobody 992 complex formed on size-exclusion chromatography. Focused refinement of cytoplasmic regions of MEGF8 (residues 2614-2749) and MGRN1 was performed to obtain this map.

Homo sapiens MOSMO 1 2

Ternary complex with MEGF8 and MGRN1 was obtained by co-expressing MEGF8, MOSMO and MGRN1 to form the MMM complex.

Homo sapiens MEGF8 1 3

MEGF8 was co-expressed with MOSMO and MGRN1, then the complex was purified on size-exclusion chromatography with nanobody 992.

Homo sapiens MGRN1 1 1

MGRN1 was co-expressed with MEGF8 and MOSMO to form the MMM complex.

Human Mahogunin Ring Finger 1 (MGRN1) E3 ligase Homo sapiens

Full-length human MGRN1 R317E with C-terminal His-6 tag.

Homo sapiens LEVO MGSILSRRIAGVEDIDIQANSAYRYPPKSGNYFASHFFMGGEKFDTPHPEGYLFGENMDLNFLGSRPVQFPYVTPAPHEP VKTLRSLVNIRKDSLRLVRYKDDADSPTEDGDKPRVLYSLEFTFDADARVAITIYCQASEEFLNGRAVYSPKSPSLQSET VHYKRGVSQQFSLPSFKIDFSEWKDDELNFDLDRGVFPVVIQAVVDEGDVVEVTGHAHVLLAAFEKHMDGSFSVKPLKQK QIVDRVSYLLQEIYGIENKNNQETKPSDDENSDNSNECVVCLSDLRDTLILPCRHLCLCTSCADTLRYQANNCPICELPF RALLQIRAVRKKPGALSPVSFSPVLAQSLEHDEHSNSDSVPPGYEPISLLEALNGLRAVSPAIPSAPLYEEITYSGISDG LSQASCPLAAIDHILDSSRQKGRPQSKAPDSTLRSPSSPIHEEDEEKLSEDVDAPPPLGGAELALRESSSPESFITEEVD ESSSPQQGTRAASIENVLQDSSPEHCGRGPPADIYLPALGPDSCSVGIDEGTKHHHHHH O60291-4 2.3.2.27 Human Modulator of Smoothened (MOSMO) Homo sapiens

Human MOSMO with C-terminal 3C protease cleavage site-TwinStrep tags. Cys164 is palmitoylated (PLM).

Homo sapiens LEVO MDKLTIISGCLFLAADIFAIASIANPDWINTGESAGALTVGLVRQCQTIHGRDRTCIPPRLPPEWVTTLFFIIMGIISLT VTCGLLVASHWRREATKYARWIAFTGMILFCMAALIFPIGFYINEVGGQPYKLPNNTVVGSSYVLFVLSIFFTIVGLLFA GKVCLPGGTLEVLFQGPGGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK Q8NHV5 Human Multiple Epidermal Growth Factor-like Domains Protein 8 (MEGF8) Homo sapiens

Human MEGF8 (residues 2312-2778) with C-terminal 1D4 epitope tag.

Homo sapiens LEVO KCQCNGHADTCNEQDGTGCPCQNNTETGTCQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTSQ TNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTSYDTFVVRVAPDTGVHTVHIQPPPAPPPPPPP ADGGPRGAGDPGGAGASSGPGAPAEPRVREVWPRGLITYVTVTEPSAVLVVRGVRDRLVITYPHEHHALKSSRFYLLLLG VGDPSGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFSCFFLFLSLCVLLWKAKQALDQRQEQRRHLQEMTKMASRPFA KVTVCFPPDPTAPASAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPAIPATTAGLRAGPITLEPTEDGMA GVATLLLQLPGGPHAPNGACLGSALVTLRHRLHEYCGGGGGAGGSGHGTGAGRKGLLSQDNLTSMSLGTETSQVAPA Q7Z7M0-2 singleParticle particle 5 7.5 150.0 NaCl sodium chloride 20.0 C8H19NO4S HEPES 2.0 C3H8O3 glycerol 2.0 CaCl2 calcium chloride 0.02 C19H36O10 glycyl-dodecyl-beta-D-maltoside (GDN)

20 mM HEPES pH 7.5, 150 mM NaCl, 2% (v/v) glycerol, 2 mM CaCl2, 0.02% (w/v) GDN

Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ETHANE 100 278 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.6 2.6 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 EPU 3.6 TFS FALCON 4i (4k x 4k) 1 11391 3.1 50.0

Images were collected in counted mode.

1 1959769

Blob picker initially was used to pick particles containing a detergent micelle.

cryoSPARC 4.3.1 Patch CTF

Patch CTF estimation was performed in cryoSPARC live pre-processing.

PHASE FLIPPING AND AMPLITUDE CORRECTION 9QRU

MMM model (9QRU PDB) and an AlphaFold2 model of nanobody 992 were merged and docked in the map using fit-in-map tool in ChimeraX.

1 C1 4.66 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 Local refinement

First, particle subtraction was performed using a mask encompassing the detergent micelle. Secondly, local refinement of cytoplasmic regions of the map (MEGF8 residues 2614-2749, MGRN1) was carried out.

83974 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 3 62596.0 cryoSPARC 4.5.3 3D classification

3D classification without alignment was performed using a mask around cytoplasmic regions of MEGF8 and MGRN1.

emd_53338.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 350.544 350.544 350.544 90.0 90.0 90.0 X Y Z -0.40522817 0.7317654 -0.0004315014 0.005947573 0.7303 0.7303 0.7303 0.1 AUTHOR ::::EMDATABANK.org::::EMD-53338:::: 9QRU PDB experimental model

The initial model consisted of chains A, B, D, F, G, H for PDB entry 9QRU.

AlphaFold in silico model

Nanobody 992

RIGID BODY FIT Coot 0.9.8.95

Initial local fitting was done using ChimeraX then manual model building in Coot was interspersed with real space refinement in Phenix.

REAL 205.300000000000011 emd_53338_msk_1.map emd_53338_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 350.544 350.544 350.544 90.0 90.0 90.0 X Y Z -0.19130233 0.36624622 -0.0001534259 0.018746017 0.7303 0.7303 0.7303 AUTHOR ::::EMDATABANK.org::::EMD-53338:::: emd_53338_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 350.544 350.544 350.544 90.0 90.0 90.0 X Y Z -0.19972147 0.41384584 -0.00015016316 0.018069673 0.7303 0.7303 0.7303 AUTHOR ::::EMDATABANK.org::::EMD-53338::::