2WFH

The Human Slit 2 Dimerization Domain D4

• PDB DOI: https://doi.org/10.2210/pdb2WFH/pdb

• Classification: SPLICING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2009-04-06 Released: 2009-04-21 
• Deposition Author(s): Seiradake, E., von Philipsborn, A.C., Henry, M., Fritz, M., Lortat-Jacob, H., Jamin, M., Hemrika, W., Bastmeyer, M., Cusack, S., McCarthy, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

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

• PubMed: 19498462 
• DOI: https://doi.org/10.1038/embor.2009.95
• Primary Citation of Related Structures:  
  2WFH


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 43.02 kDa 
• Atom Count: 3,156 
• Modelled Residue Count: 362 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SLIT HOMOLOG 2 PROTEIN C-PRODUCT	A, B	193	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O94813 (Homo sapiens) Explore O94813  Go to UniProtKB:  O94813
PHAROS:  O94813 GTEx:  ENSG00000145147

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.66	α = 90
b = 128.66	β = 90
c = 48.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Seiradake, E., von Philipsborn, A.C., Henry, M., Fritz, M., Lortat-Jacob, H., Jamin, M., Hemrika, W., Bastmeyer, M., Cusack, S., McCarthy, A.A.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-09-28
  Changes: Database references
• Version 1.3: 2018-01-10
  Changes: Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary