5AWR

Crystal structure of the SGIP1 mu homology domain in the P4212 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 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
  • Primary Citation of Related Structures:  

  • 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 Gene View: SGIP1
Go to UniProtKB:  Q9BQI5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.826α = 90.00
b = 109.826β = 90.00
c = 79.492γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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