5LXG

Revised crystal structure of the human adiponectin receptor 1 in an open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 3WXV - determined by Tanabe, H., Fujii, Y., Nakamura, Y., Hosaka, T., Okada-Iwabu, M., Iwabu, M., Kimura-Someya, T., Shirouzu, M., Yamauchi, T., Kadowaki, T., Yokoyama, S.  

Literature

Structural insights into adiponectin receptors suggest ceramidase activity.

Vasiliauskaite-Brooks, I.Sounier, R.Rochaix, P.Bellot, G.Fortier, M.Hoh, F.De Colibus, L.Bechara, C.Saied, E.M.Arenz, C.Leyrat, C.Granier, S.

(2017) Nature 6: 120-123

  • DOI: 10.1038/nature21714
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty ...

    Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty acid (FFA). The crystal structures of the two receptor subtypes, ADIPOR1 and ADIPOR2, show a similar overall seven-transmembrane-domain architecture with large unoccupied cavities and a zinc binding site within the seven transmembrane domain. However, the molecular mechanisms by which ADIPORs function are not known. Here we describe the crystal structure of ADIPOR2 bound to a FFA molecule and show that ADIPOR2 possesses intrinsic basal ceramidase activity that is enhanced by adiponectin. We also identify a ceramide binding pose and propose a possible mechanism for the hydrolytic activity of ADIPOR2 using computational approaches. In molecular dynamics simulations, the side chains of residues coordinating the zinc rearrange quickly to promote the nucleophilic attack of a zinc-bound hydroxide ion onto the ceramide amide carbonyl. Furthermore, we present a revised ADIPOR1 crystal structure exhibiting a seven-transmembrane-domain architecture that is clearly distinct from that of ADIPOR2. In this structure, no FFA is observed and the ceramide binding pocket and putative zinc catalytic site are exposed to the inner membrane leaflet. ADIPOR1 also possesses intrinsic ceramidase activity, so we suspect that the two distinct structures may represent key steps in the enzymatic activity of ADIPORs. The ceramidase activity is low, however, and further studies will be required to characterize fully the enzymatic parameters and substrate specificity of ADIPORs. These insights into ADIPOR function will enable the structure-based design of potent modulators of these clinically relevant enzymes.


    Organizational Affiliation

    Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, 34094 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adiponectin receptor protein 1
A
305Homo sapiensMutation(s): 0 
Gene Names: ADIPOR1 (PAQR1, TESBP1A)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Adiponectin Receptors
Protein: 
AdipoR1 adiponectin 1 receptor in complex with an Fv fragment
Find proteins for Q96A54 (Homo sapiens)
Go to Gene View: ADIPOR1
Go to UniProtKB:  Q96A54
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V REGION HEAVY CHAIN
H
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V REGION LIGHT CHAIN
L
107N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 92.310α = 90.00
b = 194.110β = 90.00
c = 74.330γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTERrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance647687

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references
  • Version 1.2: 2017-04-12
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Advisory, Author supporting evidence, Database references