6U5T | pdb_00006u5t

Electron cryomicroscopy Structure of S. cerevisiae FAS in the Apo state

• PDB DOI: https://doi.org/10.2210/pdb6U5T/pdb
• EM Map EMD-20655: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2019-08-28 Released: 2019-10-16 
• Deposition Author(s): Lou, J.W., Mazhab-Jafari, M.T.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase.

Lou, J.W., Iyer, K.R., Hasan, S.M.N., Cowen, L.E., Mazhab-Jafari, M.T.

(2019) Sci Rep 9: 12987-12987

• PubMed: 31506493 
• DOI: https://doi.org/10.1038/s41598-019-49261-3
• Primary Citation Related Structures: 
  6U5T, 6U5U, 6U5V, 6U5W


• PubMed Abstract: 
  

  During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.

---

Organizational Affiliation: 
• Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Institute, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Institute, Toronto, Ontario, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 439.69 kDa 
• Atom Count: 28,233 
• Modeled Residue Count: 3,649 
• Deposited Residue Count: 3,960 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit alpha	A	1,887	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1.86 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 2.3.1.41 (PDB Primary Data)
UniProt
Find proteins for A0A140KF01 (Saccharomyces cerevisiae) Explore A0A140KF01  Go to UniProtKB:  A0A140KF01

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit beta	B [auth G]	2,073	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1.86 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.9 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt
Find proteins for P07149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07149  Go to UniProtKB:  P07149

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	D [auth G]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PNS	C [auth A]	4'-PHOSPHOPANTETHEINE C11 H23 N2 O7 P S JDMUPRLRUUMCTL-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Lou, J.W., Mazhab-Jafari, M.T.

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 2.0: 2019-10-30
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary