7M7J | pdb_00007m7j

6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with antibody fragment 1B2: "turnstile closed" state (TE-free)

• PDB DOI: https://doi.org/10.2210/pdb7M7J/pdb
• EM Map EMD-23715: EMDB EMDataResource

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


• Deposited: 2021-03-28 Released: 2021-11-17 
• Deposition Author(s): Cogan, D.P., Zhang, K., Chiu, W., Khosla, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mapping the catalytic conformations of an assembly-line polyketide synthase module.

Cogan, D.P., Zhang, K., Li, X., Li, S., Pintilie, G.D., Roh, S.H., Craik, C.S., Chiu, W., Khosla, C.

(2021) Science 374: 729-734

• PubMed: 34735239 
• DOI: https://doi.org/10.1126/science.abi8358
• Primary Citation Related Structures: 
  7M7E, 7M7F, 7M7G, 7M7H, 7M7I, 7M7J


• PubMed Abstract: 
  

  Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.

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Organizational Affiliation: 
• Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 151-742, Korea.
Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94158, USA.
Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
Stanford ChEM-H, Stanford, CA 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 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: gel filtration

Macromolecule Content 

• Total Structure Weight: 439.8 kDa 
• Atom Count: 23,224 
• Modeled Residue Count: 3,124 
• Deposited Residue Count: 4,156 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EryAI	A [auth B], B [auth A]	1,593	Saccharopolyspora erythraea	Mutation(s): 0  Gene Names: eryAI EC: 2.3.1.94
UniProt
Find proteins for Q03131 (Saccharopolyspora erythraea) Explore Q03131  Go to UniProtKB:  Q03131
Find proteins for Q5UNP6 (Saccharopolyspora erythraea) Explore Q5UNP6  Go to UniProtKB:  Q5UNP6
UniProt Groups	Q5UNP6Q03131

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

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Cogan, D.P., Zhang, K., Chiu, W., 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	R01GM079429

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.2: 2025-05-21
  Changes: Data collection