31VX | pdb_000031vx

Cryo-EM structure of 3-methylcrotonyl-CoA carboxylase (MCC) complex (BC-engaged BCCP state)from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb31VX/pdb
• EM Map EMD-58684: EMDB EMDataResource

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


• Deposited: 2026-06-25 Released: 2026-09-23 
• Deposition Author(s): Yadav, A., Geibel, S.R.J.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structures of mycobacterial 3-methylcrotonyl-CoA carboxylase reveal carrier-domain translocation between catalytic sites.

Yadav, A., Florea, B.I., Geibel, S.

(2026) FEBS Lett 

• PubMed: 42723463 
• DOI: https://doi.org/10.1002/1873-3468.70453
• Primary Citation Related Structures: 
  29EX, 29GV, 31VX


• PubMed Abstract: 
  

  3-Methylcrotonyl-CoA carboxylase (MCC) catalyzes an essential step in leucine degradation. Here, we report two high-resolution cryo-EM structures of endogenous, biotin-bound Mycobacterium smegmatis AccA1-AccD1 MCC. The α ₆ β ₆ complex adopts a canonical architecture with a hexameric carboxyltransferase core flanked by trimeric biotin carboxylase modules. The structures capture BCCP engaged at either the BC or CT active site, revealing long-range carrier-domain translocation. In the CT-engaged state, local BC-domain shifts disrupt the BC-site BCCP-interaction network, disfavoring BCCP rebinding. Unlike human MCC, no comparable CT-core remodeling is observed, suggesting distinct mechanisms of carrier-domain coordination.

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Organizational Affiliation: 
• Leiden Institute of Chemistry, Leiden University, Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A6B3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 540.06 kDa 
• Atom Count: 35,644 
• Modeled Residue Count: 4,768 
• Deposited Residue Count: 5,085 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxyl transferase domain protein	A [auth D1], B [auth D2], C [auth D3], D [auth D4], E [auth D5], F [auth D6]	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 A1], H [auth A2], I [auth A3]	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)	J [auth A1], K [auth A2], L [auth A3]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-23 
Deposition Author(s): Yadav, A., Geibel, S.R.J.

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Funding Organization	Location	Grant Number
Other government	Netherlands	--

Revision History  

• Version 1.0: 2026-09-23
  Type: Initial release