5AWT

Crystal structure of the SGIP1 mu homology domain in complex with an Eps15 fragment containing two DPF motifs (YDPFGGDPFKG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 mu homology domain.

Shimada, A.Yamaguchi, A.Kohda, D.

(2016) Sci Rep 6: 19565-19565

  • DOI: 10.1038/srep19565
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • FCHo1, FCHo2, and SGIP1 are key regulators of clathrin-mediated endocytosis. Their μ homology domains (μHDs) interact with the C-terminal region of an endocytic scaffold protein, Eps15, containing fifteen Asp-Pro-Phe (DPF) motifs. Here, we show that ...

    FCHo1, FCHo2, and SGIP1 are key regulators of clathrin-mediated endocytosis. Their μ homology domains (μHDs) interact with the C-terminal region of an endocytic scaffold protein, Eps15, containing fifteen Asp-Pro-Phe (DPF) motifs. Here, we show that the high-affinity μHD-binding site in Eps15 is a region encompassing six consecutive DPF motifs, while the minimal μHD-binding unit is two consecutive DPF motifs. We present the crystal structures of the SGIP1 μHD in complex with peptides containing two DPF motifs. The peptides bind to a novel ligand-binding site of the μHD, which is distinct from those of other distantly related μHD-containing proteins. The two DPF motifs, which adopt three-dimensional structures stabilized by sequence-specific intramotif and intermotif interactions, are extensively recognized by the μHD and are both required for binding. Thus, consecutive and singly scattered DPF motifs play distinct roles in μHD binding.


    Organizational Affiliation

    Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SH3-containing GRB2-like protein 3-interacting protein 1
A
282Homo sapiensMutation(s): 0 
Gene Names: SGIP1
Find proteins for Q9BQI5 (Homo sapiens)
Go to UniProtKB:  Q9BQI5
NIH Common Fund Data Resources
PHAROS  Q9BQI5
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor substrate 15
B
11Homo sapiensMutation(s): 0 
Gene Names: EPS15AF1P
Find proteins for P42566 (Homo sapiens)
Go to UniProtKB:  P42566
NIH Common Fund Data Resources
PHAROS  P42566
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.716α = 90
b = 107.716β = 90
c = 79.978γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXT/JSPSJapanKAKENHI 20687006
MEXT/JSPSJapanKAKENHI 24687014
MEXT/JSPSJapanKAKENHI 25121726

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations