9NJU | pdb_00009nju

Structure of native homodimer of D. discoideum polyketide synthase Pks16

• PDB DOI: https://doi.org/10.2210/pdb9NJU/pdb
• EM Map EMD-49491: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Dictyostelium discoideum AX2
• Mutation(s): No 


• Deposited: 2025-02-27 Released: 2025-03-12 
• Deposition Author(s): Hoogerbrugge, G., Keatinge-Clay, A.T., Marcotte, E.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Defense (DOD, United States), Welch Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Serendipity and the slime mold: a visual survey of megadalton protein assemblies reveals the structure of the polyketide synthase Pks16

Hoogerbrugge, G., Keatinge-Clay, A.T., Marcotte, E.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 582.41 kDa 
• Atom Count: 39,352 
• Modeled Residue Count: 4,992 
• Deposited Residue Count: 5,206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable polyketide synthase 16	A, B	2,603	Dictyostelium discoideum AX2	Mutation(s): 0  EC: 2.3.1
UniProt
Find proteins for Q869W9 (Dictyostelium discoideum) Explore Q869W9  Go to UniProtKB:  Q869W9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Hoogerbrugge, G., Keatinge-Clay, A.T., Marcotte, E.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM106112
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM122480
Department of Defense (DOD, United States)	United States	W911NF-12-1-0390
Welch Foundation	United States	F-1712
Welch Foundation	United States	F-1515

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release