4WNX

Netrin 4 lacking the C-terminal Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural decoding of netrin-4 reveals a regulatory function towards mature basement membranes.

Reuten, R.Patel, T.R.McDougall, M.Rama, N.Nikodemus, D.Gibert, B.Delcros, J.G.Prein, C.Meier, M.Metzger, S.Zhou, Z.Kaltenberg, J.McKee, K.K.Bald, T.Tuting, T.Zigrino, P.Djonov, V.Bloch, W.Clausen-Schaumann, H.Poschl, E.Yurchenco, P.D.Ehrbar, M.Mehlen, P.Stetefeld, J.Koch, M.

(2016) Nat Commun 7: 13515-13515

  • DOI: 10.1038/ncomms13515
  • Primary Citation of Related Structures:  
    4WNX

  • PubMed Abstract: 
  • Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s ...

    Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies with netrin-1, netrin-4 was also proposed to play a role in neuronal outgrowth and developmental/pathological angiogenesis via interactions with netrin-1 receptors. Here, we present the high-resolution structure of netrin-4, which shows unique features in comparison with netrin-1, and show that it does not bind directly to any of the known netrin-1 receptors. We show that netrin-4 disrupts laminin networks and basement membranes (BMs) through high-affinity binding to the laminin γ1 chain. We hypothesize that this laminin-related function is essential for the previously described effects on axon growth promotion and angiogenesis. Our study unveils netrin-4 as a non-enzymatic extracellular matrix protein actively disrupting pre-existing BMs.


    Organizational Affiliation

    Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Netrin-4A433Mus musculusMutation(s): 0 
Gene Names: Ntn4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JI33 (Mus musculus)
Explore Q9JI33 
Go to UniProtKB:  Q9JI33
IMPC:  MGI:1888978
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB, C2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TAM
Query on TAM

Download Ideal Coordinates CCD File 
G [auth A]TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.755α = 90
b = 75.049β = 96.07
c = 74.672γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building
PHASERphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary