6FKQ

THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A FRAGMENT OF DRAXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC.

Liu, Y.Bhowmick, T.Liu, Y.Gao, X.Mertens, H.D.T.Svergun, D.I.Xiao, J.Zhang, Y.Wang, J.H.Meijers, R.

(2018) Neuron 97: 1261-1267.e4

  • DOI: 10.1016/j.neuron.2018.02.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and ...

    Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Netrin-1
A
415Homo sapiensMutation(s): 0 
Gene Names: NTN1 (NTN1L)
Find proteins for O95631 (Homo sapiens)
Go to Gene View: NTN1
Go to UniProtKB:  O95631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Draxin
B
19Homo sapiensMutation(s): 0 
Gene Names: DRAXIN (C1orf187)
Find proteins for Q8NBI3 (Homo sapiens)
Go to Gene View: DRAXIN
Go to UniProtKB:  Q8NBI3
Small Molecules
Ligands 4 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 130.794α = 90.00
b = 130.794β = 90.00
c = 183.870γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marie Curie CoFUNDGermany--

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references