9EYT

Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-1 peptide (LIDL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.186 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast.

Defelipe, L.A.Veith, K.Burastero, O.Kupriianova, T.Bento, I.Skruzny, M.Kolbel, K.Uetrecht, C.Thuenauer, R.Garcia-Alai, M.M.

(2024) Nat Commun 15: 9655-9655

  • DOI: https://doi.org/10.1038/s41467-024-54037-z
  • Primary Citation of Related Structures:  
    9EX5, 9EXF, 9EXG, 9EXT, 9EYT

  • PubMed Abstract: 

    Clathrin forms a triskelion, or three-legged, network that regulates cellular processes by facilitating cargo internalization and trafficking in eukaryotes. Its N-terminal domain is crucial for interacting with adaptor proteins, which link clathrin to the membrane and engage with specific cargo. The N-terminal domain contains up to four adaptor-binding sites, though their role in preferential occupancy by adaptor proteins remains unclear. In this study, we examine the binding hierarchy of adaptors for clathrin, using integrative biophysical and structural approaches, along with in vivo functional experiments. We find that yeast epsin Ent5 has the highest affinity for clathrin, highlighting its key role in cellular trafficking. Epsins Ent1 and Ent2, crucial for endocytosis but thought to have redundant functions, show distinct binding patterns. Ent1 exhibits stronger interactions with clathrin than Ent2, suggesting a functional divergence toward actin binding. These results offer molecular insights into adaptor protein selectivity, suggesting they competitively bind clathrin while also targeting three different clathrin sites.


  • Organizational Affiliation

    European Molecular Biology Laboratory - Hamburg Unit, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Clathrin heavy chain373Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CHC1YGL206C
UniProt
Find proteins for P22137 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22137 
Go to UniProtKB:  P22137
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22137
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Epsin-1B [auth E],
C [auth G],
D [auth M]
7Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12518 
Go to UniProtKB:  Q12518
Entity Groups  
UniProt GroupQ12518
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.31α = 90
b = 56.31β = 90
c = 254.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union664726

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references