5KVM

Extracellular region of mouse GPR56/ADGRG1 in complex with FN3 monobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.449 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains.

Salzman, G.S.Ackerman, S.D.Ding, C.Koide, A.Leon, K.Luo, R.Stoveken, H.M.Fernandez, C.G.Tall, G.G.Piao, X.Monk, K.R.Koide, S.Arac, D.

(2016) Neuron 91: 1292-1304

  • DOI: 10.1016/j.neuron.2016.08.022

  • PubMed Abstract: 
  • Adhesion G protein-coupled receptors (aGPCRs) play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. aGPCRs have large alternatively spliced extracellular regions (ECRs) that likely medi ...

    Adhesion G protein-coupled receptors (aGPCRs) play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. aGPCRs have large alternatively spliced extracellular regions (ECRs) that likely mediate intercellular signaling; however, the precise roles of ECRs remain unclear. The aGPCR GPR56/ADGRG1 regulates both oligodendrocyte and cortical development. Accordingly, human GPR56 mutations cause myelination defects and brain malformations. Here, we determined the crystal structure of the GPR56 ECR, the first structure of any complete aGPCR ECR, in complex with an inverse-agonist monobody, revealing a GPCR-Autoproteolysis-Inducing domain and a previously unidentified domain that we term Pentraxin/Laminin/neurexin/sex-hormone-binding-globulin-Like (PLL). Strikingly, PLL domain deletion caused increased signaling and characterizes a GPR56 splice variant. Finally, we show that an evolutionarily conserved residue in the PLL domain is critical for oligodendrocyte development in vivo. Thus, our results suggest that the GPR56 ECR has unique and multifaceted regulatory functions, providing novel insights into aGPCR roles in neurobiology.


    Organizational Affiliation

    Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. Electronic address: arac@uchicago.edu.,Biophysical Sciences Program, The University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. Electronic address: shohei.koide@nyumc.org.,Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.,Departments of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adhesion G-protein coupled receptor G1
A
355Mus musculusMutation(s): 0 
Gene Names: Adgrg1 (Cyt28, Gpr56)
Find proteins for Q8K209 (Mus musculus)
Go to UniProtKB:  Q8K209
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Adhesion G-protein coupled receptor G1
B
9Mus musculusMutation(s): 0 
Gene Names: Adgrg1 (Cyt28, Gpr56)
Find proteins for Q8K209 (Mus musculus)
Go to UniProtKB:  Q8K209
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FN3 monobody alpha5
C
95N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.449 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • Space Group: P 65
  • Diffraction Data DOI: 
    10.15785/SBGRID/421 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 120.336α = 90.00
b = 120.336β = 90.00
c = 72.850γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CRANK2phasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF30-GM116455
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54-GM087519
Brain Research FoundationUnited States--

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references