4PLO | pdb_00004plo

Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5)

  • Classification: PROTEIN BINDING
  • Organism(s): Mus musculus, Gallus gallus
  • Expression System: Homo sapiens
  • 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: 2.90 Å
  • R-Value Free: 
    0.288 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4PLO

Ligand Structure Quality Assessment 


This is version 1.6 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 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.

Macromolecule Content 

  • Total Structure Weight: 72.5 kDa 
  • Atom Count: 4,868 
  • Modeled Residue Count: 604 
  • Deposited Residue Count: 638 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Netrin receptor DCCA [auth B]206Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P70211 (Mus musculus)
Explore P70211 
Go to UniProtKB:  P70211
IMPC:  MGI:94869
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70211
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Netrin-1B [auth A]432Gallus 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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.288 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.478α = 90
b = 72.939β = 90
c = 285.159γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.6: 2024-11-20
    Changes: Structure summary