6POL

Crystal structure of the human NELL1 EGF1-3-Robo3 FN1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance.

Pak, J.S.DeLoughery, Z.J.Wang, J.Acharya, N.Park, Y.Jaworski, A.Ozkan, E.

(2020) Nat Commun 11: 1489-1489

  • DOI: https://doi.org/10.1038/s41467-020-15211-1
  • Primary Citation of Related Structures:  
    6POG, 6POK, 6POL

  • PubMed Abstract: 

    Axon pathfinding is critical for nervous system development, and it is orchestrated by molecular cues that activate receptors on the axonal growth cone. Robo family receptors bind Slit guidance cues to mediate axon repulsion. In mammals, the divergent family member Robo3 does not bind Slits, but instead signals axon repulsion from its own ligand, NELL2. Conversely, canonical Robos do not mediate NELL2 signaling. Here, we present the structures of NELL-Robo3 complexes, identifying a mode of ligand engagement for Robos that is orthogonal to Slit binding. We elucidate the structural basis for differential binding between NELL and Robo family members and show that NELL2 repulsive activity is a function of its Robo3 affinity and is enhanced by ligand trimerization. Our results reveal a mechanism of oligomerization-induced Robo activation for axon guidance and shed light on Robo family member ligand binding specificity, conformational variability, divergent modes of signaling, and evolution.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Roundabout homolog 3
A, C, E
114Homo sapiensMutation(s): 0 
Gene Names: ROBO3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MS0 (Homo sapiens)
Explore Q96MS0 
Go to UniProtKB:  Q96MS0
GTEx:  ENSG00000154134 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96MS0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C-binding protein NELL1
B, D, F
139Homo sapiensMutation(s): 0 
Gene Names: NELL1NRP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92832 (Homo sapiens)
Explore Q92832 
Go to UniProtKB:  Q92832
GTEx:  ENSG00000165973 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92832
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q92832-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth B],
Q [auth D],
Y [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth B],
T [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
G [auth A]
H [auth A]
K [auth B]
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
K [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
S [auth D],
U [auth E],
V [auth E],
W [auth E],
X [auth E]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth B],
R [auth D],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87α = 90
b = 87β = 90
c = 211.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS097161

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary