9CJL

Molecular basis of TMED9 dodecamer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway.

Xiao, L.Pi, X.Goss, A.C.El-Baba, T.Ehrmann, J.F.Grinkevich, E.Bazua-Valenti, S.Padovano, V.Alper, S.L.Carey, D.Udeshi, N.D.Carr, S.A.Pablo, J.L.Robinson, C.V.Greka, A.Wu, H.

(2024) Sci Adv 10: eadp2221-eadp2221

  • DOI: https://doi.org/10.1126/sciadv.adp2221
  • Primary Citation of Related Structures:  
    9CJK, 9CJL

  • PubMed Abstract: 

    Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargos in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here, we report cryo-electron microscopy structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers, and, by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of coat protein I (COPI), but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane emp24 domain-containing protein 9
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
235Homo sapiensMutation(s): 0 
Gene Names: TMED9GP25L2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVK6 (Homo sapiens)
Explore Q9BVK6 
Go to UniProtKB:  Q9BVK6
PHAROS:  Q9BVK6
GTEx:  ENSG00000184840 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVK6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9ED (Subject of Investigation/LOI)
Query on 9ED

Download Ideal Coordinates CCD File 
M [auth B],
N [auth H]
[(2R)-2-[(E)-octadec-9-enoyl]oxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] (E)-octadec-9-enoate
C45 H85 O19 P3
IGQSAMXNWMLOOS-ZLFOHRMWSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release