Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.18 kDa 
• Atom Count: 5505 
• Residue Count: 634 
• Unique protein chains: 1

4YMK

Crystal Structure of Stearoyl-Coenzyme A Desaturase 1

• DOI: 10.2210/pdb4YMK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-03-06 Released: 2015-06-24 
• Deposition Author(s): Bai, Y., McCoy, J.G., Rajashankar, K.R., Zhou, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

Literature

X-ray structure of a mammalian stearoyl-CoA desaturase.

Bai, Y., McCoy, J.G., Levin, E.J., Sobrado, P., Rajashankar, K.R., Fox, B.G., Zhou, M.

(2015) Nature 524: 252-256

• PubMed: 26098370 
• DOI: 10.1038/nature14549
• Primary Citation of Related Structures:  
  4YMK


• PubMed Abstract: 
  

Stearoyl-CoA desaturase (SCD) is conserved in all eukaryotes and introduces the first double bond into saturated fatty acyl-CoAs. Because the monounsaturated products of SCD are key precursors of membrane phospholipids, cholesterol esters and triglycerides, SCD is pivotal in fatty acid metabolism. Humans have two SCD homologues (SCD1 and SCD5), while mice have four (SCD1-SCD4). SCD1-deficient mice do not become obese or diabetic when fed a high-fat diet because of improved lipid metabolic profiles and insulin sensitivity. Thus, SCD1 is a pharmacological target in the treatment of obesity, diabetes and other metabolic diseases. SCD1 is an integral membrane protein located in the endoplasmic reticulum, and catalyses the formation of a cis-double bond between the ninth and tenth carbons of stearoyl- or palmitoyl-CoA. The reaction requires molecular oxygen, which is activated by a di-iron centre, and cytochrome b5, which regenerates the di-iron centre. To understand better the structural basis of these characteristics of SCD function, here we crystallize and solve the structure of mouse SCD1 bound to stearoyl-CoA at 2.6 Å resolution. The structure shows a novel fold comprising four transmembrane helices capped by a cytosolic domain, and a plausible pathway for lateral substrate access and product egress. The acyl chain of the bound stearoyl-CoA is enclosed in a tunnel buried in the cytosolic domain, and the geometry of the tunnel and the conformation of the bound acyl chain provide a structural basis for the regioselectivity and stereospecificity of the desaturation reaction. The dimetal centre is coordinated by a unique spacial arrangement of nine conserved histidine residues that implies a potentially novel mechanism for oxygen activation. The structure also illustrates a possible route for electron transfer from cytochrome b5 to the di-iron centre.

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Organizational Affiliation: 

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA desaturase 1	A, D	339	Mus musculus	Mutation(s): 0  Gene Names: Scd1 EC: 1.14.19.1
Find proteins for P13516 (Mus musculus) Explore P13516  Go to UniProtKB:  P13516

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ST9	A, D	STEAROYL-COENZYME A C39 H70 N7 O17 P3 S SIARJEKBADXQJG-LFZQUHGESA-N
MPG	A, D	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C21 H40 O4 JPJYKWFFJCWMPK-GDCKJWNLSA-N
ZN	A, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.061	α = 90
b = 113.766	β = 90
c = 141.698	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
SHELXDE	phasing
PHASER	phasing
HKL-2000	data scaling
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-03-06 
• Released Date: 2015-06-24 
Deposition Author(s): Bai, Y., McCoy, J.G., Rajashankar, K.R., Zhou, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM098878

Revision History 

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2015-07-08
  Changes: Structure summary
• Version 1.2: 2015-08-19
  Changes: Database references
• Version 1.3: 2016-06-08
  Changes: Atomic model
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.5: 2017-11-22
  Changes: Refinement description
• Version 1.6: 2019-12-25
  Changes: Author supporting evidence