2WFH

The Human Slit 2 Dimerization Domain D4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and functional relevance of the Slit2 homodimerization domain.

Seiradake, E.von Philipsborn, A.C.Henry, M.Fritz, M.Lortat-Jacob, H.Jamin, M.Hemrika, W.Bastmeyer, M.Cusack, S.McCarthy, A.A.

(2009) EMBO Rep. 10: 736-741

  • DOI: 10.1038/embor.2009.95

  • PubMed Abstract: 
  • Slit proteins are secreted ligands that interact with the Roundabout (Robo) receptors to provide important guidance cues in neuronal and vascular development. Slit-Robo signalling is mediated by an interaction between the second Slit domain and the f ...

    Slit proteins are secreted ligands that interact with the Roundabout (Robo) receptors to provide important guidance cues in neuronal and vascular development. Slit-Robo signalling is mediated by an interaction between the second Slit domain and the first Robo domain, as well as being dependent on heparan sulphate. In an effort to understand the role of the other Slit domains in signalling, we determined the crystal structure of the fourth Slit2 domain (D4) and examined the effects of various Slit2 constructs on chick retinal ganglion cell axons. Slit2 D4 forms a homodimer using the conserved residues on its concave face, and can also bind to heparan sulphate. We observed that Slit2 D4 frequently results in growth cones with collapsed lamellipodia and that this effect can be inhibited by exogenously added heparan sulphate. Our results show that Slit2 D4-heparan sulphate binding contributes to a Slit-Robo signalling mechanism more intricate than previously thought.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SLIT HOMOLOG 2 PROTEIN C-PRODUCT
A, B
193Homo sapiensMutation(s): 0 
Gene Names: SLIT2 (SLIL3)
Find proteins for O94813 (Homo sapiens)
Go to Gene View: SLIT2
Go to UniProtKB:  O94813
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 128.660α = 90.00
b = 128.660β = 90.00
c = 48.150γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-09-28
    Type: Database references
  • Version 1.3: 2018-01-10
    Type: Database references