8GKC

Atomic model of the core modifying region of human fatty acid synthase in complex with TVB-2640 - C2 refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic model for core modifying region of human fatty acid synthase in complex with Denifanstat.

Hasan, S.M.N.Lou, J.W.Keszei, A.F.A.Dai, D.L.Mazhab-Jafari, M.T.

(2023) Nat Commun 14: 3460-3460

  • DOI: https://doi.org/10.1038/s41467-023-39266-y
  • Primary Citation of Related Structures:  
    8EYI, 8EYK, 8GKC

  • PubMed Abstract: 

    Fatty acid synthase (FASN) catalyzes the de novo synthesis of palmitate, a 16-carbon chain fatty acid that is the primary precursor of lipid metabolism and an important intracellular signaling molecule. FASN is an attractive drug target in diabetes, cancer, fatty liver diseases, and viral infections. Here, we develop an engineered full-length human FASN (hFASN) that enables isolation of the condensing and modifying regions of the protein post-translation. The engineered protein enables electron cryo-microscopy (cryoEM) structure determination of the core modifying region of hFASN to 2.7 Å resolution. Examination of the dehydratase dimer within this region reveals that unlike its close homolog, porcine FASN, the catalytic cavity is close-ended and is accessible only through one opening in the vicinity of the active site. The core modifying region exhibits two major global conformational variabilities that describe long-range bending and twisting motions of the complex in solution. Finally, we solved the structure of this region bound to an anti-cancer drug, Denifanstat (i.e., TVB-2640), demonstrating the utility of our approach as a platform for structure guided design of future hFASN small molecule inhibitors.


  • Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid synthaseA,
B [auth D]
1,670Homo sapiensMutation(s): 0 
Gene Names: FASNFAS
EC: 2.3.1.85 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 2.3.1.41 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49327 (Homo sapiens)
Explore P49327 
Go to UniProtKB:  P49327
PHAROS:  P49327
GTEx:  ENSG00000169710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49327
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
X5O BindingDB:  8GKC IC50: min: 52, max: 180 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.0.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada419240
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-06070

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection