4PLM

Crystal Structure of Chicken Netrin-1 (LN-LE3)

  • Classification: PROTEIN BINDING
  • Organism(s): Gallus gallus
  • Expression System: Baculoviridae
  • Mutation(s): No 

  • Deposited: 2014-05-18 Released: 2014-06-18 
  • Deposition Author(s): Xu, K., Nikolov, D.B.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.257 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.7 of the entry. See complete history


Literature

Neural migration. Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism.

Xu, K.Wu, Z.Renier, N.Antipenko, A.Tzvetkova-Robev, D.Xu, Y.Minchenko, M.Nardi-Dei, V.Rajashankar, K.R.Himanen, J.Tessier-Lavigne, M.Nikolov, D.B.

(2014) Science 344: 1275-1279

  • DOI: https://doi.org/10.1126/science.1255149
  • Primary Citation of Related Structures:  
    4PLM, 4PLN, 4PLO

  • PubMed Abstract: 

    Netrins are secreted proteins that regulate axon guidance and neuronal migration. Deleted in colorectal cancer (DCC) is a well-established netrin-1 receptor mediating attractive responses. We provide evidence that its close relative neogenin is also a functional netrin-1 receptor that acts with DCC to mediate guidance in vivo. We determined the structures of a functional netrin-1 region, alone and in complexes with neogenin or DCC. Netrin-1 has a rigid elongated structure containing two receptor-binding sites at opposite ends through which it brings together receptor molecules. The ligand/receptor complexes reveal two distinct architectures: a 2:2 heterotetramer and a continuous ligand/receptor assembly. The differences result from different lengths of the linker connecting receptor domains fibronectin type III domain 4 (FN4) and FN5, which differs among DCC and neogenin splice variants, providing a basis for diverse signaling outcomes.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Netrin-1432Gallus gallusMutation(s): 0 
Gene Names: NTN1
UniProt
Find proteins for Q90922 (Gallus gallus)
Explore Q90922 
Go to UniProtKB:  Q90922
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90922
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.627α = 90
b = 62.627β = 90
c = 269.788γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Derived calculations
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.6: 2023-12-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.7: 2024-10-16
    Changes: Structure summary