9QF9 | pdb_00009qf9

Structure of the GH13 domain of Ruminococcus bromii Amy16

• PDB DOI: https://doi.org/10.2210/pdb9QF9/pdb
• EM Map EMD-53102: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Ruminococcus bromii L2-63
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-11 Released: 2025-10-22 
• Deposition Author(s): Wimmer, B.H., Medalia, O.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon.

Wimmer, B.H., Morais, S., Amit, I., Tovar-Herrera, O., Tatli, M., Trautwein-Schult, A., Pfister, B., Zalk, R., Todtli, P., Simoni, S., Lisibach, M., Levin, L., Becher, D., Bayer, E.A., Medalia, O., Mizrahi, I.

(2025) Nat Commun 16: 10763-10763

• PubMed: 41298524 
• DOI: https://doi.org/10.1038/s41467-025-65800-1
• Primary Citation Related Structures: 
  9QF3, 9QF8, 9QF9, 9QFA


• PubMed Abstract: 
  

  Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic complex. To unravel its architecture, function, and the interplay among its components, we applied a holistic multilayered approach: Cryo-electron tomography reveals that the amylosome comprises a constitutive extracellular layer extending toward the RS substrate. Proteomics demonstrates remodeling of its contents across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses reveal complementarity and synergistic RS degradation by these enzymes. We demonstrate that amylosome composition and RS degradation are regulated at two levels: structural constraints and expression-driven shifts in enzyme proportions enforce enzyme proximity, which allows R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, Zurich, Switzerland.
Department of Life Sciences, Ben-Gurion-University of the Negev, Beer-Sheva, Israel.
National Institute of Biotechnology in the Negev, Ben-Gurion-University of the Negev, Be'er Sheva, Israel.
The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany.
Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland.
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
Department of Biochemistry, University of Zurich, Zurich, Switzerland. [e-mail].
Department of Life Sciences, Ben-Gurion-University of the Negev, Beer-Sheva, Israel. [e-mail].
National Institute of Biotechnology in the Negev, Ben-Gurion-University of the Negev, Be'er Sheva, Israel. [e-mail].
The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 93.29 kDa 
• Atom Count: 3,219 
• Modeled Residue Count: 417 
• Deposited Residue Count: 851 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ruminococcus bromii Amy16	A	851	Ruminococcus bromii L2-63	Mutation(s): 0  Gene Names: SPE92332.1 EC: 3.2.1.1
UniProt
Find proteins for A0A2N0UZV9 (Ruminococcus bromii) Explore A0A2N0UZV9  Go to UniProtKB:  A0A2N0UZV9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Wimmer, B.H., Medalia, O.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	10000885

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references