9FGM | pdb_00009fgm

Cryo-EM structure of Legionella effector SdeC (3D flexible refinement)

• PDB DOI: https://doi.org/10.2210/pdb9FGM/pdb
• EM Map EMD-50413: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-24 Released: 2025-06-04 
• Deposition Author(s): Weng, T.-H., Misra, M., Chen, W., Safarian, S., Kudryashev, M., Dikic, I.
• Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

BAR-like C-terminal domain of Legionella SidE family is crucial for its membrane localization and secretion

Misra, M., Mukherjee, R., Bhattacharya, A., Chen, W., Weng, T.-H., van Ek, L., Cristiani, A., Li, C., Mohammed, A., Liu, Y., Pomirska, J., Vidov, A., Heden van Noort, G., Bhaskara, R., Svergun, D., Gavin, A.C., Safarian, S., Kudryashev, M., Luo, Z.-Q., Dikic, I.

To be published.

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: 199.47 kDa 
• Atom Count: 9,032 
• Modeled Residue Count: 1,135 
• Deposited Residue Count: 1,764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SdeC	A	1,764	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for Q6RCQ8 (Legionella pneumophila) Explore Q6RCQ8  Go to UniProtKB:  Q6RCQ8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Weng, T.-H., Misra, M., Chen, W., Safarian, S., Kudryashev, M., Dikic, I.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	742720
German Research Foundation (DFG)	Germany	253130777

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release
  
• Version 1.1: 2025-06-18
  Changes: Data collection