30BU | pdb_000030bu

Cryo-EM structure of ComEC from Neomoorella carbonis

• PDB DOI: https://doi.org/10.2210/pdb30BU/pdb
• EM Map EMD-57549: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Neomoorella carbonis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-04-20 Released: 2026-05-20 
• Deposition Author(s): Deselaers, S., Wang, D., Cairoli, T., Afanasyev, P., Hospenthal, M.K.
• Funding Organization(s): Swiss State Secretariat for Education, Research and Innovation, Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure and biochemistry reveal substrate-modulated ComEC nuclease activity during DNA processing.

Deselaers, S., Wang, D., Cairoli, T., Afanasyev, P., Hospenthal, M.K.

(2026) Nucleic Acids Res 54

• PubMed: 42689412 
• DOI: https://doi.org/10.1093/nar/gkag861
• Primary Citation Related Structures: 
  30BT, 30BU, 32KS


• PubMed Abstract: 
  

  Natural transformation enables bacteria to internalize extracellular DNA, driving adaptation and the spread of antibiotic resistance. The membrane protein ComEC mediates translocation of single-stranded DNA (ssDNA) across the cytoplasmic membrane while degrading the complementary strand, yet the structural basis of its activity remains incompletely defined. Here, we report a cryo-electron microscopy structure of full-length ComEC from Neomoorella carbonis in a pre-translocation state, revealing a three-domain architecture and a conserved transmembrane channel captured in a closed conformation. Structural analysis indicates that conformational rearrangements of channel-lining helices would be required to accommodate ssDNA. Biochemical assays show that, relative to the isolated β-lactamase-like domain, full-length ComEC degrades DNA more efficiently and exhibits position-dependent cleavage of phosphodiester bonds within the DNA substrate. Importantly, coating of the DNA by the periplasmic DNA receptor ComEA suppresses endonucleolytic cleavage and enhances 5'' terminal cleavage, thereby directing ComEC towards productive processing of transforming DNA during natural transformation.

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Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland.
CryoHub, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
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: 175.33 kDa 
• Atom Count: 7,929 
• Modeled Residue Count: 1,024 
• Deposited Residue Count: 1,602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ComEC	A, B	801	Neomoorella carbonis	Mutation(s): 0
UniProt
Find proteins for A0A6I5ZRL0 (Neomoorella glycerini) Explore A0A6I5ZRL0  Go to UniProtKB:  A0A6I5ZRL0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	1.21.2-5419
MODEL REFINEMENT	Rosetta	3.14

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Deselaers, S., Wang, D., Cairoli, T., Afanasyev, P., Hospenthal, M.K.

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Funding Organization	Location	Grant Number
Swiss State Secretariat for Education, Research and Innovation	Switzerland	MB22.00043
Swiss National Science Foundation	Switzerland	3200-0-239918

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release
  
• Version 1.1: 2026-09-16
  Changes: Data collection, Database references