6KS0

Crystal structure of the human adiponectin receptor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human adiponectin receptor AdipoR1 assumes closed and open structures.

Tanabe, H.Fujii, Y.Okada-Iwabu, M.Iwabu, M.Kano, K.Kawana, H.Hato, M.Nakamura, Y.Terada, T.Kimura-Someya, T.Shirouzu, M.Kawano, Y.Yamamoto, M.Aoki, J.Yamauchi, T.Kadowaki, T.Yokoyama, S.

(2020) Commun Biol 3: 446-446

  • DOI: https://doi.org/10.1038/s42003-020-01160-4
  • Primary Citation of Related Structures:  
    6KRZ, 6KS0, 6KS1

  • PubMed Abstract: 

    The human adiponectin receptors, AdipoR1 and AdipoR2, are key anti-diabetic molecules. We previously reported the crystal structures of human AdipoR1 and AdipoR2, revealing that their seven transmembrane helices form an internal closed cavity (the closed form). In this study, we determined the crystal structure of the D208A variant AdipoR1, which is fully active with respect to the major downstream signaling. Among the three molecules in the asymmetric unit, two assume the closed form, and the other adopts the open form with large openings in the internal cavity. Between the closed- and open-form structures, helices IV and V are tilted with their intracellular ends shifted by about 4 and 11 Å, respectively. Furthermore, we reanalyzed our previous wild-type AdipoR1 diffraction data, and determined a 44:56 mixture of the closed and open forms, respectively. Thus, we have clarified the closed-open interconversion of AdipoR1, which may be relevant to its functional mechanism(s).


  • Organizational Affiliation

    RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.


Macromolecules
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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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
The heavy chain variable domain (Antibody)B [auth H]119Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
The light chain variable domain (Antibody)C [auth L]107Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.663α = 90
b = 194.443β = 90
c = 74.384γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP17am010108
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16K18509

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description