7R86

Structure of mouse BAI1 (ADGRB1) in complex with mouse Nogo receptor (RTN4R)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


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Literature

RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development.

Wang, J.Miao, Y.Wicklein, R.Sun, Z.Wang, J.Jude, K.M.Fernandes, R.A.Merrill, S.A.Wernig, M.Garcia, K.C.Sudhof, T.C.

(2021) Cell 184: 5869-5885.e25

  • DOI: 10.1016/j.cell.2021.10.016
  • Primary Citation of Related Structures:  
    7R84, 7R85, 7R86

  • PubMed Abstract: 
  • RTN4-binding proteins were widely studied as "NoGo" receptors, but their physiological interactors and roles remain elusive. Similarly, BAI adhesion-GPCRs were associated with numerous activities, but their ligands and functions remain unclear. Using unbiased approaches, we observed an unexpected convergence: RTN4 receptors are high-affinity ligands for BAI adhesion-GPCRs ...

    RTN4-binding proteins were widely studied as "NoGo" receptors, but their physiological interactors and roles remain elusive. Similarly, BAI adhesion-GPCRs were associated with numerous activities, but their ligands and functions remain unclear. Using unbiased approaches, we observed an unexpected convergence: RTN4 receptors are high-affinity ligands for BAI adhesion-GPCRs. A single thrombospondin type 1-repeat (TSR) domain of BAIs binds to the leucine-rich repeat domain of all three RTN4-receptor isoforms with nanomolar affinity. In the 1.65 Å crystal structure of the BAI1/RTN4-receptor complex, C-mannosylation of tryptophan and O-fucosylation of threonine in the BAI TSR-domains creates a RTN4-receptor/BAI interface shaped by unusual glycoconjugates that enables high-affinity interactions. In human neurons, RTN4 receptors regulate dendritic arborization, axonal elongation, and synapse formation by differential binding to glial versus neuronal BAIs, thereby controlling neural network activity. Thus, BAI binding to RTN4/NoGo receptors represents a receptor-ligand axis that, enabled by rare post-translational modifications, controls development of synaptic circuits.


    Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: tcs1@stanford.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reticulon-4 receptorA, B285Mus musculusMutation(s): 0 
Gene Names: Rtn4rNgr1Nogor
UniProt
Find proteins for Q99PI8 (Mus musculus)
Explore Q99PI8 
Go to UniProtKB:  Q99PI8
Entity Groups  
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UniProt GroupQ99PI8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vasculostatin-120C, D54Mus musculusMutation(s): 0 
Gene Names: Adgrb1Bai1
UniProt & NIH Common Fund Data Resources
Find proteins for Q3UHD1 (Mus musculus)
Explore Q3UHD1 
Go to UniProtKB:  Q3UHD1
IMPC:  MGI:1933736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3UHD1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranoseE, F 2N/AO-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G36855WW
GlyCosmos:  G36855WW
GlyGen:  G36855WW
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
Q [auth B],
R [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
J [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
AA [auth D],
W [auth C],
X [auth C],
Z [auth D]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
PAB
Query on PAB

Download Ideal Coordinates CCD File 
I [auth A]4-AMINOBENZOIC ACID
C7 H7 N O2
ALYNCZNDIQEVRV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
S [auth B],
T [auth B],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
U [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth A],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 10.15785/SBGRID/856
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.468α = 90
b = 95.315β = 105.39
c = 69.682γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references