9YX0 | pdb_00009yx0

Structure of the 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb9YX0/pdb
• EM Map EMD-73568: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2025-10-26 Released: 2025-11-26 
• Deposition Author(s): Liang, Y., Rubinstein, J.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex

Liang, Y., Rubinstein, J.L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 751.23 kDa 
• Atom Count: 47,381 
• Modeled Residue Count: 6,588 
• Deposited Residue Count: 7,092 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxyl transferase domain protein	A [auth G], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L]	513	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R1D9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1D9  Go to UniProtKB:  A0R1D9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
biotin carboxylase	G [auth D], H [auth B], I [auth C], J [auth A], K [auth F], L [auth E]	669	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  EC: 6.3.4.14
UniProt
Find proteins for A0R1D8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1D8  Go to UniProtKB:  A0R1D8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN (Subject of Investigation/LOI)	M [auth D], N [auth B], O [auth C], P [auth A], Q [auth F], R [auth E]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC	5.0.0-privatebeta

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Liang, Y., Rubinstein, J.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT191893

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release