7NE0

Structure of the ternary complex between Netrin-1, Repulsive-Guidance Molecule-B (RGMB) and Neogenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling.

Robinson, R.A.Griffiths, S.C.van de Haar, L.L.Malinauskas, T.van Battum, E.Y.Zelina, P.Schwab, R.A.Karia, D.Malinauskaite, L.Brignani, S.van den Munkhof, M.H.Dudukcu, O.De Ruiter, A.A.Van den Heuvel, D.M.A.Bishop, B.Elegheert, J.Aricescu, A.R.Pasterkamp, R.J.Siebold, C.

(2021) Cell 184: 2103

  • DOI: https://doi.org/10.1016/j.cell.2021.02.045
  • Primary Citation of Related Structures:  
    7NDG, 7NE0, 7NE1

  • PubMed Abstract: 

    During cell migration or differentiation, cell surface receptors are simultaneously exposed to different ligands. However, it is often unclear how these extracellular signals are integrated. Neogenin (NEO1) acts as an attractive guidance receptor when the Netrin-1 (NET1) ligand binds, but it mediates repulsion via repulsive guidance molecule (RGM) ligands. Here, we show that signal integration occurs through the formation of a ternary NEO1-NET1-RGM complex, which triggers reciprocal silencing of downstream signaling. Our NEO1-NET1-RGM structures reveal a "trimer-of-trimers" super-assembly, which exists in the cell membrane. Super-assembly formation results in inhibition of RGMA-NEO1-mediated growth cone collapse and RGMA- or NET1-NEO1-mediated neuron migration, by preventing formation of signaling-compatible RGM-NEO1 complexes and NET1-induced NEO1 ectodomain clustering. These results illustrate how simultaneous binding of ligands with opposing functions, to a single receptor, does not lead to competition for binding, but to formation of a super-complex that diminishes their functional outputs.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Netrin-1444Homo sapiensMutation(s): 0 
Gene Names: NTN1NTN1L
UniProt & NIH Common Fund Data Resources
Find proteins for O95631 (Homo sapiens)
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Go to UniProtKB:  O95631
PHAROS:  O95631
GTEx:  ENSG00000065320 
Entity Groups  
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UniProt GroupO95631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neogenin354Mus musculusMutation(s): 0 
Gene Names: Neo1
UniProt
Find proteins for Q7TQG5 (Mus musculus)
Explore Q7TQG5 
Go to UniProtKB:  Q7TQG5
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UniProt GroupQ7TQG5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Repulsive Guidance Molecule B35Homo sapiensMutation(s): 0 
Gene Names: RGMB
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Find proteins for Q6NW40 (Homo sapiens)
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Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
GTEx:  ENSG00000174136 
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UniProt GroupQ6NW40
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Repulsive Guidance Molecule B C-terminal region (chain D)165Homo sapiensMutation(s): 0 
Gene Names: RGMB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens)
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Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
GTEx:  ENSG00000174136 
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UniProt GroupQ6NW40
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranoseE [auth I],
F [auth J],
G [auth K],
H [auth L]
2N/A
Glycosylation Resources
GlyTouCan:  G97555GV
GlyCosmos:  G97555GV
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.78α = 90
b = 136.78β = 90
c = 430.11γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC20724/A14414
Cancer Research UKUnited KingdomC20724/A26752
European Research Council (ERC)United Kingdom647278
Medical Research Council (MRC, United Kingdom)United KingdomMR/L017776/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description