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- PDB-31vx: Cryo-EM structure of 3-methylcrotonyl-CoA carboxylase (MCC) compl... -

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Basic information

Entry
Database: PDB / ID: 31vx
TitleCryo-EM structure of 3-methylcrotonyl-CoA carboxylase (MCC) complex (BC-engaged BCCP state)from Mycobacterium smegmatis
Components
  • Carboxyl transferase domain protein
  • biotin carboxylase
KeywordsLIGASE / Biotin carboxyalse
Function / homology
Function and homology information


methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / biotin carboxylase / biotin carboxylase activity / L-leucine catabolic process / transferase activity / metal ion binding / ATP binding
Similarity search - Function
: / Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. ...: / Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
BIOTIN / biotin carboxylase / Carboxyl transferase domain protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsYadav, A. / Geibel, S.R.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: FEBS Lett / Year: 2026
Title: Structures of mycobacterial 3-methylcrotonyl-CoA carboxylase reveal carrier-domain translocation between catalytic sites.
Authors: Ajit Yadav / Bogdan I Florea / Sebastian Geibel /
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 ...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 αβ 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.
History
DepositionJun 25, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D1: Carboxyl transferase domain protein
D2: Carboxyl transferase domain protein
D3: Carboxyl transferase domain protein
D4: Carboxyl transferase domain protein
D5: Carboxyl transferase domain protein
D6: Carboxyl transferase domain protein
A1: biotin carboxylase
A2: biotin carboxylase
A3: biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,06412
Polymers539,3319
Non-polymers7333
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Carboxyl transferase domain protein


Mass: 54816.199 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R1D9
#2: Protein biotin carboxylase


Mass: 70144.711 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R1D8, biotin carboxylase
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Purifed from soluble fraction / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12970 / Symmetry type: POINT
Atomic model buildingDetails: CryFold / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005636388
ELECTRON MICROSCOPYf_angle_d0.571349525
ELECTRON MICROSCOPYf_chiral_restr0.04565612
ELECTRON MICROSCOPYf_plane_restr0.00476565
ELECTRON MICROSCOPYf_dihedral_angle_d12.708413088

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