9CD4 | pdb_00009cd4

Cryo-EM structure of Candidatus Saccharibacterium phosphoketolase complexed with 2-acetyl-thiamine diphosphate

• PDB DOI: https://doi.org/10.2210/pdb9CD4/pdb
• EM Map EMD-45462: EMDB EMDataResource

• Classification: LYASE
• Organism(s): Candidatus Saccharimonadota bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2025-08-06 
• Deposition Author(s): Singal, B., Landwehr, G., Jewett, M.C.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

A synthetic cell-free pathway for biocatalytic upgrading of one-carbon substrates.

Landwehr, G.M., Vogeli, B., Tian, C., Singal, B., Gupta, A., Lion, R., Sargent, E.H., Karim, A.S., Jewett, M.C.

(2024) bioRxiv 

• PubMed: 39149402 
• DOI: https://doi.org/10.1101/2024.08.08.607227
• Primary Citation of Related Structures:  
  9CD3, 9CD4


• PubMed Abstract: 
  

  Biotechnological processes hold tremendous potential for the efficient and sustainable conversion of one-carbon (C1) substrates into complex multi-carbon products. However, the development of robust and versatile biocatalytic systems for this purpose remains a significant challenge. In this study, we report a hybrid electrochemical-biochemical cell-free system for the conversion of C1 substrates into the universal biological building block acetyl-CoA. The synthetic reductive formate pathway (ReForm) consists of five core enzymes catalyzing non-natural reactions that were established through a cell-free enzyme engineering platform. We demonstrate that ReForm works in a plug-and-play manner to accept diverse C1 substrates including CO ₂ equivalents. We anticipate that ReForm will facilitate efforts to build and improve synthetic C1 utilization pathways for a formate-based bioeconomy.

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Organizational Affiliation: 
• Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
Stanford SLAC CryoEM Initiative, Stanford University; Stanford, CA 94305, USA.
Department of Bioengineering, Stanford University; Stanford, CA 94305, USA.

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: 181.55 kDa 
• Atom Count: 12,598 
• Modeled Residue Count: 1,570 
• Deposited Residue Count: 1,598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoketolase family protein	A [auth C], B [auth D]	799	Candidatus Saccharimonadota bacterium	Mutation(s): 0  Gene Names: HG452_002440

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HTL (Subject of Investigation/LOI)	C, D	2-ACETYL-THIAMINE DIPHOSPHATE C14 H21 N4 O8 P2 S GYRGKLZCJRVYRV-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Singal, B., Landwehr, G., Jewett, M.C.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0023278

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-11-26
  Changes: Data collection, Database references