4DOU

Crystal Structure of a Single-chain Trimer of Human Adiponectin Globular Domain

• PDB DOI: https://doi.org/10.2210/pdb4DOU/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-02-10 Released: 2012-02-29 
• Deposition Author(s): Min, X., Walker, N.P., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Crystal structure of a single-chain trimer of human adiponectin globular domain.

Min, X., Lemon, B., Tang, J., Liu, Q., Zhang, R., Walker, N., Li, Y., Wang, Z.

(2012) FEBS Lett 586: 912-917

• PubMed: 22449980 
• DOI: https://doi.org/10.1016/j.febslet.2012.02.024
• Primary Citation of Related Structures:  
  4DOU


• PubMed Abstract: 
  

  Adiponectin is increasingly recognized as a potential therapeutic agent for the treatment of diabetes and other metabolic diseases. It circulates in plasma as homotrimers and higher-order oliogomers of homotrimers. To facilitate the production of active recombinant adiponectin as a therapeutic tool, we designed a single-chain globular domain adiponectin (sc-gAd) in which three monomer sequences are linked together in tandem to form one contiguous polypeptide. Here, we present the crystal structure of human sc-gAd at 2.0Å resolution. The structure reveals a similar trimeric topology to that of mouse gAd protein. Trimer formation is further rigidified by three calcium ions.

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Organizational Affiliation: 

Department of Molecular Structure, Amgen Inc., South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.55 kDa 
• Atom Count: 3,486 
• Modelled Residue Count: 399 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adiponectin	A	442	Homo sapiens	Mutation(s): 0  Gene Names: ADIPOQ, ACDC, ACRP30, APM1, GBP28, adiponectin
UniProt & NIH Common Fund Data Resources
Find proteins for Q15848 (Homo sapiens) Explore Q15848  Go to UniProtKB:  Q15848
PHAROS:  Q15848 GTEx:  ENSG00000181092

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.31	α = 117.23
b = 49.63	β = 101.68
c = 50.46	γ = 105.31

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Min, X., Walker, N.P., Wang, Z.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Database references
• Version 1.2: 2017-05-31
  Changes: Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description