8TJO | pdb_00008tjo

Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in complex with antibody fragment 1B2: Crosslinked Intra-State 1

• PDB DOI: https://doi.org/10.2210/pdb8TJO/pdb
• EM Map EMD-41306: EMDB EMDataResource

• Classification: BIOSYNTHETIC PROTEIN/IMMUNE SYSTEM
• Organism(s): Saccharopolyspora erythraea, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-23 Released: 2024-07-24 
• Deposition Author(s): Cogan, D.P., Soohoo, A.M., Chen, M., Brodsky, K.L., Liu, Y., Khosla, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis for intermodular communication in assembly-line polyketide biosynthesis.

Cogan, D.P., Soohoo, A.M., Chen, M., Liu, Y., Brodsky, K.L., Khosla, C.

(2025) Nat Chem Biol 21: 876-882

• PubMed: 39179672 
• DOI: https://doi.org/10.1038/s41589-024-01709-y
• Primary Citation Related Structures: 
  8TJN, 8TJO, 8TJP, 8TKO, 8TPW, 8TPX


• PubMed Abstract: 
  

  Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. To investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain-domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.

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Organizational Affiliation: 
• Department of Chemistry, Stanford University, Stanford, CA, USA. [e-mail].
Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA. [e-mail].
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA. [e-mail].
Department of Chemical Engineering, Stanford University, Stanford, CA, USA. [e-mail].
Stanford ChEM-H, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 482.11 kDa 
• Atom Count: 22,287 
• Modeled Residue Count: 2,992 
• Deposited Residue Count: 4,538 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6	A, B	1,784	Saccharopolyspora erythraea	Mutation(s): 0  Gene Names: eryAI, eryA EC: 2.3.1.94
UniProt
Find proteins for Q03131 (Saccharopolyspora erythraea) Explore Q03131  Go to UniProtKB:  Q03131
Find proteins for Q03133 (Saccharopolyspora erythraea) Explore Q03133  Go to UniProtKB:  Q03133
UniProt Groups	Q03131Q03133

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fragment 1B2, Heavy Chain	C, E	249	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fragment 1B2, Light Chain	D, F	236	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4HH	A, B	L-PEPTIDE LINKING	C14 H28 N3 O9 P S		SER

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.61 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: 2024-07-24 
Deposition Author(s): Cogan, D.P., Soohoo, A.M., Chen, M., Brodsky, K.L., Liu, Y., Khosla, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM141799
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM136039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM129541
National Science Foundation (NSF, United States)	United States	DGE-1656518

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Data collection, Database references
• Version 1.2: 2025-06-11
  Changes: Data collection, Database references, Structure summary