5LXG | pdb_00005lxg

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 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LXG

This is version 1.6 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3WXV

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: https://doi.org/10.1038/nature21714
  • Primary Citation Related Structures: 
    5LWY, 5LX9, 5LXA, 5LXG

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 60.11 kDa 
  • Atom Count: 4,213 
  • Modeled Residue Count: 508 
  • Deposited Residue Count: 531 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adiponectin receptor protein 1305Homo sapiensMutation(s): 0 
Gene Names: ADIPOR1PAQR1TESBP1ACGI-45
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96A54 (Homo sapiens)
Explore Q96A54 
Go to UniProtKB:  Q96A54
PHAROS:  Q96A54
GTEx:  ENSG00000159346 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96A54
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
V REGION HEAVY CHAINB [auth H]119Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
V REGION LIGHT CHAINC [auth L]107Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.234 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.31α = 90
b = 194.11β = 90
c = 74.33γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance647687

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-04-12
    Changes: Database references
  • Version 1.3: 2018-01-31
    Changes: Advisory, Author supporting evidence, Database references
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 1.5: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.6: 2024-10-16
    Changes: Structure summary