9WFD | pdb_00009wfd

Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus

• PDB DOI: https://doi.org/10.2210/pdb9WFD/pdb
• EM Map EMD-65926: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Acidithiobacillus caldus SM-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-21 Released: 2025-11-19 
• Deposition Author(s): Liu, R.H., Zhang, K., Feng, Q.S., Dai, X., Zhang, X., Li, W., Bao, Z.P., Lin, W.F., Fu, Y., Li, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Unveiling Acidophilic Secretin Nanopores for Ion Exclusion and Single-Molecule Sensing

Liu, R., Zhang, K., Feng, Q., He, S., Fan, Q., Zhang, X., Li, W., Bao, Z., Lin, W., Fu, Y., Li, Y.

(2025) Adv Funct Mater 

• DOI: https://doi.org/10.1002/adfm.202517259

Biological Assembly 1  

Global Symmetry: Cyclic - C14  (Explore in 3D)
Global Stoichiometry: Homo 14-mer - A14 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 749.79 kDa 
• Atom Count: 45,332 
• Modeled Residue Count: 6,034 
• Deposited Residue Count: 7,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II and III secretion system protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N	502	Acidithiobacillus caldus SM-1	Mutation(s): 0  Gene Names: Atc_2749
UniProt
Find proteins for F9ZTP9 (Acidithiobacillus caldus (strain SM-1)) Explore F9ZTP9  Go to UniProtKB:  F9ZTP9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Liu, R.H., Zhang, K., Feng, Q.S., Dai, X., Zhang, X., Li, W., Bao, Z.P., Lin, W.F., Fu, Y., Li, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release