9PC6 | pdb_00009pc6

Antibody (1B2) Bound Crosslinked Rifamycin Synthetase Module 1 with a C-terminal Type II Thioesterase

• PDB DOI: https://doi.org/10.2210/pdb9PC6/pdb
• EM Map EMD-71497: EMDB EMDataResource

• Classification: Transferase/Immune System
• Organism(s): Amycolatopsis mediterranei, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-27 Released: 2025-07-23 
• Deposition Author(s): Cogan, D.P., Liu, C., West, R.C., Chen, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.96 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

C-terminal dimerization motifs control asynchronous chain elongation during modular polyketide biosynthesis.

Liu, C., West, R.C., Chen, M., Cohn, W., Wang, G., Kim, S., Mandot, A.M., Faull, K.F., Cogan, D.P.

(2026) J Biol Chem 302: 113119-113119

• PubMed: 42103224 
• DOI: https://doi.org/10.1016/j.jbc.2026.113119
• Primary Citation Related Structures: 
  9PAT, 9PAV, 9PC6


• PubMed Abstract: 
  

  The rifamycin synthetase (RIFS) from the bacterium Amycolatopsis mediterranei is a homodimeric assembly line that catalyzes 40+ chemical reactions to generate a complex precursor of the antitubercular drug rifampicin. It consists of an N-terminal substrate loading module followed by a decamodular polyketide synthase (PKS). While the catalytic functions are known for each domain of RIFS, how these activities are spatially and temporally coordinated during polyketide assembly remains incompletely defined. Here, we address this problem with thiol-selective crosslinking to understand the basis for conformational asymmetry during polyketide chain elongation. Our data suggest that C-terminal dimerization motifs-which are ubiquitous in bacterial PKS assembly lines-force their adjacent substrate carrier protein (CP) domains to comigrate between two equivalent ketosynthase (KS) active site chambers. Cryogenic electron microscopy analysis of the first PKS module of RIFS further underscored this observation while revealing its unique architecture. Single-turnover kinetic analysis indicated that although changes to the C-terminus that reduced CP dimerization supported 2-fold greater KS:CP interactions, they were insufficient to overcome substoichiometric product accumulation on the homodimeric protein. Our findings illuminate factors underlying asymmetry during polyketide antibiotic biosynthesis and should be instructive to future megasynth(et)ase engineers.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content 

• Total Structure Weight: 496.34 kDa 
• Atom Count: 29,408 
• Modeled Residue Count: 3,977 
• Deposited Residue Count: 4,708 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-deoxyerythronolide-B synthase,RifR	A, B	1,869	Amycolatopsis mediterranei	Mutation(s): 0  Gene Names: rifA, rifR EC: 2.3.1.94 (PDB Primary Data), 2.3.1.41 (UniProt)
UniProt
Find proteins for O54666 (Amycolatopsis mediterranei) Explore O54666  Go to UniProtKB:  O54666
Find proteins for Q7BUF9 (Amycolatopsis mediterranei) Explore Q7BUF9  Go to UniProtKB:  Q7BUF9
UniProt Groups	O54666Q7BUF9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fragment 1B2 Heavy Chain	C [auth J], D [auth K]	249	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fragment 1B2 Light Chain	E [auth I], F [auth L]	236	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
4HH	A, B	SER	4-Phosphopantetheine	C14 H28 N3 O9 P S

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.96 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.0
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Cogan, D.P., Liu, C., West, R.C., Chen, M.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release
  
• Version 2.0: 2026-02-04
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2026-09-30
  Changes: Data collection, Database references