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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9WFD

This is version 1.0 of the entry. See complete history.

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

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

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II and III secretion system protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9ZTP9
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.