7NDG

Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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-1A,
F [auth G],
I [auth D]
441Homo sapiensMutation(s): 0 
Gene Names: NTN1NTN1L
UniProt & NIH Common Fund Data Resources
Find proteins for O95631 (Homo sapiens)
Explore O95631 
Go to UniProtKB:  O95631
PHAROS:  O95631
GTEx:  ENSG00000065320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NeogeninB,
G [auth H],
J [auth E]
354Mus musculusMutation(s): 0 
Gene Names: Neo1
UniProt
Find proteins for Q7TQG5 (Mus musculus)
Explore Q7TQG5 
Go to UniProtKB:  Q7TQG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7TQG5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Repulsive Guidance Molecule B (C-terminal region)C [auth F],
E [auth C],
K [auth I]
252Homo sapiensMutation(s): 0 
Gene Names: RGMB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens)
Explore Q6NW40 
Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
GTEx:  ENSG00000174136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NW40
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RGM domain family member BD [auth N],
H [auth M],
L [auth O]
119Homo sapiensMutation(s): 0 
Gene Names: RGMB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens)
Explore Q6NW40 
Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
GTEx:  ENSG00000174136 
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UniProt GroupQ6NW40
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth E]
N [auth A]
O [auth A]
P [auth A]
Q [auth B]
AA [auth E],
N [auth A],
O [auth A],
P [auth A],
Q [auth B],
S [auth G],
T [auth G],
U [auth G],
V [auth H],
X [auth D],
Y [auth D],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A],
R [auth G],
W [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.18.2.

Structure Validation

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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
Medical Research Council (MRC, United Kingdom)United KingdomMR/L009609/1
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/15
Wellcome TrustUnited Kingdom099675/Z/12/Z
Wellcome TrustUnited Kingdom090532/Z/09/Z
Netherlands Organisation for Scientific Research (NWO)NetherlandsALW-VICI
H2020 Marie Curie Actions of the European CommissionNetherlands289581

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 2.0: 2021-04-28
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary