21AK | pdb_000021ak

Cryo-EM structure of the E. coli ArnA hexamer

• PDB DOI: https://doi.org/10.2210/pdb21AK/pdb
• EM Map EMD-67448: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-12-04 Released: 2026-03-25 
• Deposition Author(s): Jiang, X., Kikkawa, M.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Cryo-EM reveals ArnA contamination during purification of a ciliary protein complex

Jiang, X., Kikkawa, M.

(2026) Acta Crystallogr D Biol Crystallogr 

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 892.63 kDa 
• Atom Count: 28,592 
• Modeled Residue Count: 3,612 
• Deposited Residue Count: 7,920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional polymyxin resistance protein ArnA	A, B, C, D, E, F, G, H, I, J, K, L	660	Escherichia coli	Mutation(s): 0  Gene Names: arnA, pmrI, yfbG, b2255, JW2249 EC: 2.1.2.13 (PDB Primary Data), 1.1.1.305 (PDB Primary Data)
UniProt
Find proteins for P77398 (Escherichia coli (strain K12)) Explore P77398  Go to UniProtKB:  P77398

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.7.1
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Jiang, X., Kikkawa, M.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER2202
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H05247
Japan Society for the Promotion of Science (JSPS)	Japan	JP24KF0141
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K18106

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release