2026-06-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_abbrev _citation.journal_id_CSD _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_abbrev _citation.journal_id_CSD _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.page_first _em_admin.last_update 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 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 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 Mol.Cell US 86 2207 2026 42190653 doi:10.1016/j.molcel.2026.05.001 1097-2765 2168 MOCEFL EMD-53336 focused EM volume

Focused refinement of transmembrane and extracellular map regions (MOSMO, MEGF8 residues 2374-2610, nanobody 992).

EMD-53337 focused EM volume

Focused refinement of the extracellular map regions (MOSMO, MEGF8 residues 2374-2580, nanobody 992).

EMD-53338 focused EM volume

Focused refinement of the cytoplasmic map regions (MEGF8 residues 2614-2749, MGRN1).

EMD-53339 consensus EM volume

Consensus map for focused refinements of the MMM-nanobody 992 complex.

9qsh FULLOVERLAP PDB 9QRU unspecified

9QRU contains the same MEGF8-MOSMO-MGRN1 (MMM) protein complexed with a different nanobody (nanobody 270).

PDB 9QS6 unspecified

9QS6 contains the same MEGF8-MOSMO-MGRN1 (MMM) protein complexed with a different nanobody (nanobody 270) and MEGF8 contains a mutated cytoplasmic helix (termed "helix-stabilized" construct).

EMDB EMD-53336 focused EM volume

Focused refinement of transmembrane and extracellular map regions (MOSMO, MEGF8 residues 2374-2610, nanobody 992).

EMDB EMD-53337 focused EM volume

Focused refinement of the extracellular map regions (MOSMO, MEGF8 residues 2374-2580, nanobody 992).

EMDB EMD-53338 focused EM volume

Focused refinement of the cytoplasmic map regions (MEGF8 residues 2614-2749, MGRN1).

EMDB EMD-53339 consensus EM volume

Consensus map for focused refinements of the MMM-nanobody 992 complex.

EMDB EMD-53340 associated EM volume

Structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)

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 4

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.

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 Nanobody 992 1 4 Lama glama MGRN1 1 1

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

Homo sapiens Isoform 4 of E3 ubiquitin-protein ligase MGRN1 Homo sapiens 0.05945498799999999

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

1 Homo sapiens LEVO MGSILSRRIAGVEDIDIQANSAYRYPPKSGNYFASHFFMGGEKFDTPHPEGYLFGENMDLNFLGSRPVQFPYVTPAPHEP VKTLRSLVNIRKDSLRLVRYKDDADSPTEDGDKPRVLYSLEFTFDADARVAITIYCQASEEFLNGRAVYSPKSPSLQSET VHYKRGVSQQFSLPSFKIDFSEWKDDELNFDLDRGVFPVVIQAVVDEGDVVEVTGHAHVLLAAFEKHMDGSFSVKPLKQK QIVDRVSYLLQEIYGIENKNNQETKPSDDENSDNSNECVVCLSDLRDTLILPCRHLCLCTSCADTLRYQANNCPICELPF RALLQIRAVRKKPGALSPVSFSPVLAQSLEHDEHSNSDSVPPGYEPISLLEALNGLRAVSPAIPSAPLYEEITYSGISDG LSQASCPLAAIDHILDSSRQKGRPQSKAPDSTLRSPSSPIHEEDEEKLSEDVDAPPPLGGAELALRESSSPESFITEEVD ESSSPQQGTRAASIENVLQDSSPEHCGRGPPADIYLPALGPDSCSVGIDEGTKHHHHHH O60291 2.3.2.27 Modulator of smoothened protein Homo sapiens 0.022594246

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

1 Homo sapiens LEVO MDKLTIISGCLFLAADIFAIASIANPDWINTGESAGALTVGLVRQCQTIHGRDRTCIPPRLPPEWVTTLFFIIMGIISLT VTCGLLVASHWRREATKYARWIAFTGMILFCMAALIFPIGFYINEVGGQPYKLPNNTVVGSSYVLFVLSIFFTIVGLLFA GKVCLPGGTLEVLFQGPGGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK Q8NHV5 Isoform 2 of Multiple epidermal growth factor-like domains protein 8 Homo sapiens 0.05035297699999999

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

1 Homo sapiens LEVO KCQCNGHADTCNEQDGTGCPCQNNTETGTCQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTSQ TNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTSYDTFVVRVAPDTGVHTVHIQPPPAPPPPPPP ADGGPRGAGDPGGAGASSGPGAPAEPRVREVWPRGLITYVTVTEPSAVLVVRGVRDRLVITYPHEHHALKSSRFYLLLLG VGDPSGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFSCFFLFLSLCVLLWKAKQALDQRQEQRRHLQEMTKMASRPFA KVTVCFPPDPTAPASAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPAIPATTAGLRAGPITLEPTEDGMA GVATLLLQLPGGPHAPNGACLGSALVTLRHRLHEYCGGGGGAGGSGHGTGAGRKGLLSQDNLTSMSLGTETSQVAPA Q7Z7M0 Nanobody 992 Lama glama 0.013833138999999998

Nanobody 992 with C-terminal His6-EPEA tags.

1 Escherichia coli K-12 LEVO QVQLVESGGGLVQVGGSLTLSCAASGRIFNIDGMGWFRQAAGKQSEWVAGVSKDGSRNYEDFAKGRFTVSRDNAKNTVYL QMNNLKPEDTAVYYCAVRIDNGDDYWGQGTQVTVSSHHHHHHEPEA ZINC ION 6.5409e-05 2 ZN PALMITIC ACID 0.00025642399999999994 1 PLM (1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-16-methoxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane] 0.000428647 1 A1JAX water 1.8015e-05 6 HOH 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 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.

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.

C1 3.5 OTHER cryoSPARC 4.5.1 Local refinement

Using map alone (d99), resolution was estimated in Phenix real-space refinement of the composite map.

187459 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 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

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

REAL