5ON7

The ENTH domain from epsin-2 in complex with phosphatidylinositol 4,5-bisphosphate (PIP2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.287 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Epsin and Sla2 form assemblies through phospholipid interfaces.

Garcia-Alai, M.M.Heidemann, J.Skruzny, M.Gieras, A.Mertens, H.D.T.Svergun, D.I.Kaksonen, M.Uetrecht, C.Meijers, R.

(2018) Nat Commun 9: 328-328

  • DOI: https://doi.org/10.1038/s41467-017-02443-x
  • Primary Citation of Related Structures:  
    5ON7, 5ONF, 5OO7, 6ENR

  • PubMed Abstract: 

    In clathrin-mediated endocytosis, adapter proteins assemble together with clathrin through interactions with specific lipids on the plasma membrane. However, the precise mechanism of adapter protein assembly at the cell membrane is still unknown. Here, we show that the membrane-proximal domains ENTH of epsin and ANTH of Sla2 form complexes through phosphatidylinositol 4,5-bisphosphate (PIP2) lipid interfaces. Native mass spectrometry reveals how ENTH and ANTH domains form assemblies by sharing PIP2 molecules. Furthermore, crystal structures of epsin Ent2 ENTH domain from S. cerevisiae in complex with PIP2 and Sla2 ANTH domain from C. thermophilum illustrate how allosteric phospholipid binding occurs. A comparison with human ENTH and ANTH domains reveal only the human ENTH domain can form a stable hexameric core in presence of PIP2, which could explain functional differences between fungal and human epsins. We propose a general phospholipid-driven multifaceted assembly mechanism tolerating different adapter protein compositions to induce endocytosis.


  • Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epsin-2
A, B
156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENT2YLR206W
Membrane Entity: Yes 
UniProt
Find proteins for Q05785 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05785 
Go to UniProtKB:  Q05785
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05785
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO
Query on PIO

Download Ideal Coordinates CCD File 
C [auth A][(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.287 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.357α = 90
b = 211.357β = 90
c = 211.357γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection