3VIA

Crystal structure of the PH domain of Evectin-2 from human


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2

Okazaki, S.Kato, R.Uchida, Y.Taguchi, T.Arai, H.Wakatsuki, S.

(2012) Acta Crystallogr.,Sect.D 68: 117-123

  • DOI: 10.1107/S0907444911051626

  • PubMed Abstract: 
  • Evectin-2 is a recycling endosomal protein involved in retrograde transport. Its primary sequence contains an N-terminal pleckstrin homology (PH) domain and a C-terminal hydrophobic region. The PH domain of evectin-2 can specifically bind phosphatidy ...

    Evectin-2 is a recycling endosomal protein involved in retrograde transport. Its primary sequence contains an N-terminal pleckstrin homology (PH) domain and a C-terminal hydrophobic region. The PH domain of evectin-2 can specifically bind phosphatidylserine, which is enriched in recycling endosomes, and plays an essential role in retrograde transport from recycling endosomes to the trans-Golgi network. The structure of human evectin-2 PH domain in complex with O-phospho-L-serine has recently been reported and demonstrates how the head group of phosphatidylserine is recognized. However, it was not possible to elucidate from the structure why evectin-2 cannot bind phosphatidic acid or phosphatidylethanolamine, which share a common moiety with phosphatidylserine. Here, the crystal structure at 1.75 Å resolution of an apo form of human evectin-2 PH domain, in which the ligand-binding site is free from crystal packing and is thus appropriate for comparison with the structure of the complex, is reported. Comparison between the structures of the apo form and the O-phospho-L-serine complex revealed ligand-induced conformational change evoked by interaction between the carboxyl moiety of the head group of phosphatidylserine and the main-chain N atom of Thr14. This structural change effectively explains the strict ligand specificity of the PH domain of human evectin-2.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pleckstrin homology domain-containing family B member 2
A, B
112Homo sapiensMutation(s): 0 
Gene Names: PLEKHB2 (EVT2)
Find proteins for Q96CS7 (Homo sapiens)
Go to Gene View: PLEKHB2
Go to UniProtKB:  Q96CS7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.283α = 90.00
b = 54.267β = 90.00
c = 111.638γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-08
    Type: Database references