9QSH | pdb_00009qsh

Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9QSH

This is version 1.2 of the entry. See complete history

Literature

Design principles of a membrane-spanning ubiquitin ligase.

Williams, C.Nocka, L.M.Hedger, G.Parashara, P.Pardon, E.Latorraca, N.R.Pusapati, G.V.Sarkar, P.Lartey, D.Gao, L.Milenkovic, L.Chalk, R.Steyaert, J.Marqusee, S.Carrique, L.Bazan, J.F.Rouse, S.L.Kong, J.H.Siebold, C.Rohatgi, R.

(2026) Mol Cell 86: 2207

  • DOI: https://doi.org/10.1016/j.molcel.2026.05.001
  • Primary Citation Related Structures: 
    9QQS, 9QRU, 9QS6, 9QSH, 9QTY

  • PubMed 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 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.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 147.05 kDa 
  • Atom Count: 7,267 
  • Modeled Residue Count: 923 
  • Deposited Residue Count: 1,353 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 4 of E3 ubiquitin-protein ligase MGRN1A [auth D]539Homo sapiensMutation(s): 1 
Gene Names: MGRN1KIAA0544RNF156
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O60291 (Homo sapiens)
Explore O60291 
Go to UniProtKB:  O60291
PHAROS:  O60291
GTEx:  ENSG00000102858 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60291
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Modulator of smoothened proteinB [auth A]211Homo sapiensMutation(s): 0 
Gene Names: MOSMOATTHOGC16orf52
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHV5 (Homo sapiens)
Explore Q8NHV5 
Go to UniProtKB:  Q8NHV5
PHAROS:  Q8NHV5
GTEx:  ENSG00000185716 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NHV5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Multiple epidermal growth factor-like domains protein 8C [auth B]477Homo sapiensMutation(s): 0 
Gene Names: MEGF8C19orf49EGFL4KIAA0817
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7M0 (Homo sapiens)
Explore Q7Z7M0 
Go to UniProtKB:  Q7Z7M0
PHAROS:  Q7Z7M0
GTEx:  ENSG00000105429 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z7M0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 992D [auth C]126Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.5.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomDRCRPG-May23/100002
Cancer Research UKUnited KingdomC20724/A26752
Wellcome TrustUnited Kingdom218482/Z/19/Z
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom093305/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Data collection, Database references
  • Version 1.2: 2026-06-17
    Changes: Data collection, Database references