6ZYF

Notum_Ghrelin complex

• PDB DOI: https://doi.org/10.2210/pdb6ZYF/pdb

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


• Deposited: 2020-07-31 Released: 2021-03-10 
• Deposition Author(s): Zhao, Y., Jones, E.Y.
• Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.252 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Literature

Notum deacylates octanoylated ghrelin.

Zhao, Y., Schuhmacher, L.N., Roberts, M., Kakugawa, S., Bineva-Todd, G., Howell, S., O'Reilly, N., Perret, C., Snijders, A.P., Vincent, J.P., Jones, E.Y.

(2021) Mol Metab 49: 101201-101201

• PubMed: 33647468 
• DOI: https://doi.org/10.1016/j.molmet.2021.101201
• Primary Citation of Related Structures:  
  6ZYF


• PubMed Abstract: 
  

  The only proteins known to be modified by O-linked lipidation are Wnts and ghrelin, and enzymatic removal of this post-translational modification inhibits ligand activity. Indeed, the Wnt-deacylase activity of Notum is the basis of its ability to act as a feedback inhibitor of Wnt signalling. Whether Notum also deacylates ghrelin has not been determined.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.1 kDa 
• Atom Count: 5,730 
• Modelled Residue Count: 701 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Palmitoleoyl-protein carboxylesterase NOTUM	A, B	383	Homo sapiens	Mutation(s): 0  Gene Names: NOTUM, OK/SW-CL.30 EC: 3.1.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P988 (Homo sapiens) Explore Q6P988  Go to UniProtKB:  Q6P988
PHAROS:  Q6P988 GTEx:  ENSG00000185269

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
K4Q (Subject of Investigation/LOI)	D [auth A], F [auth B]	[(2~{S})-2-azanyl-3-oxidanylidene-propyl] octanoate C11 H21 N O3 CSUFCBOFZFUZNV-SNVBAGLBSA-N
EDO	G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.252 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.418	α = 90
b = 184.072	β = 90
c = 61.811	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Zhao, Y., Jones, E.Y.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C375/A17721
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/M000141/1

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references
• Version 1.2: 2021-04-07
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Database references, Refinement description