9KKM | pdb_00009kkm

cryo-EM structure of acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP

• PDB DOI: https://doi.org/10.2210/pdb9KKM/pdb
• EM Map EMD-62392: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-11-13 Released: 2025-11-19 
• Deposition Author(s): Wang, W., Han, S.R., Xu, Y.Y., Gao, H.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryo-EM structure of acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP

Wang, W., Han, S.R., Xu, Y.Y., Gao, H.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 336.41 kDa 
• Atom Count: 21,254 
• Modeled Residue Count: 2,722 
• Deposited Residue Count: 3,034 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA carboxylase multifunctional enzyme AccADCB	A, B	1,517	Shewanella oneidensis MR-1	Mutation(s): 1  Gene Names: accADCB, SO_0840 EC: 6.3.4.14 (PDB Primary Data), 6.4.1.2 (PDB Primary Data)
UniProt
Find proteins for Q8EIJ9 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EIJ9  Go to UniProtKB:  Q8EIJ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Wang, W., Han, S.R., Xu, Y.Y., Gao, H.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

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