7ND2

Cryo-EM structure of the human FERRY complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of mRNA binding by the human FERRY Rab5 effector complex.

Quentin, D.Schuhmacher, J.S.Klink, B.U.Lauer, J.Shaikh, T.R.Huis In 't Veld, P.J.Welp, L.M.Urlaub, H.Zerial, M.Raunser, S.

(2023) Mol Cell 83: 1856-1871.e9

  • DOI: https://doi.org/10.1016/j.molcel.2023.05.009
  • Primary Citation of Related Structures:  
    7ND2, 8A3O, 8A3P

  • PubMed Abstract: 

    The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals a unique clamp-like architecture that bears no resemblance to any known structure of Rab effectors. A combination of functional and mutational studies reveals that while the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. Our study provides mechanistic insights into long-distance mRNA transport and demonstrates that the particular architecture of FERRY is closely linked to a previously undescribed mode of RNA binding, involving coiled-coil domains.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 1 regulatory subunit 21A,
F [auth B]
784Homo sapiensMutation(s): 0 
Gene Names: PPP1R21CCDC128KLRAQ1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMI0 (Homo sapiens)
Explore Q6ZMI0 
Go to UniProtKB:  Q6ZMI0
PHAROS:  Q6ZMI0
GTEx:  ENSG00000162869 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZMI0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Quinone oxidoreductase-like protein 1B [auth C],
E [auth D]
356Homo sapiensMutation(s): 0 
Gene Names: CRYZL14P11
EC: 1
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Find proteins for O95825 (Homo sapiens)
Explore O95825 
Go to UniProtKB:  O95825
PHAROS:  O95825
GTEx:  ENSG00000205758 
Entity Groups  
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UniProt GroupO95825
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine amidotransferase-like class 1 domain-containing protein 1C [auth E],
D [auth F],
G [auth H],
H [auth G]
227Homo sapiensMutation(s): 0 
Gene Names: GATD1PDDC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB37 (Homo sapiens)
Explore Q8NB37 
Go to UniProtKB:  Q8NB37
PHAROS:  Q8NB37
GTEx:  ENSG00000177225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NB37
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONSPHIRE

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)615984

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection