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- EMDB-58684: Cryo-EM structure of 3-methylcrotonyl-CoA carboxylase (MCC) compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-58684
TitleCryo-EM structure of 3-methylcrotonyl-CoA carboxylase (MCC) complex (BC-engaged BCCP state)from Mycobacterium smegmatis
Map dataBC-engaged BCCP state of MCC complex
Sample
  • Complex: Purifed from soluble fraction
    • Protein or peptide: Carboxyl transferase domain protein
    • Protein or peptide: biotin carboxylase
  • Ligand: BIOTIN
KeywordsBiotin carboxyalse / LIGASE
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 carboxylase / Carboxyl transferase domain protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsYadav A / Geibel SRJ
Funding support Netherlands, 1 items
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, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58684.png

Downloads & links

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Map

FileDownload / File: emd_58684.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBC-engaged BCCP state of MCC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 416 pix.
= 401.282 Å		0.96 Å/pix.
x 416 pix.
= 401.282 Å		0.96 Å/pix.
x 416 pix.
= 401.282 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum0.0 - 0.7305121
Average (Standard dev.)0.005570029 (±0.019741073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 401.28192 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_58684_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_58684_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purifed from soluble fraction

EntireName: Purifed from soluble fraction
Components
  • Complex: Purifed from soluble fraction
    • Protein or peptide: Carboxyl transferase domain protein
    • Protein or peptide: biotin carboxylase
  • Ligand: BIOTIN

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Supramolecule #1: Purifed from soluble fraction

SupramoleculeName: Purifed from soluble fraction / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Carboxyl transferase domain protein

MacromoleculeName: Carboxyl transferase domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 54.816199 KDa
SequenceString: MSSHRDEHLA LVAELRSKLA AAALGGPERA RERHVGRGKL LPRDRVDGLL DPGSPFLELA PLAAGGMYDD ECPGAGMIAG IGRVSGREC VIVANDATVK GGTYYPITVK KHLRAQEIAL QNKLPCIYLV DSGGAFLPRQ DEVFPDRDHF GRIFYNQATM S AQGIAQIA ...String:
MSSHRDEHLA LVAELRSKLA AAALGGPERA RERHVGRGKL LPRDRVDGLL DPGSPFLELA PLAAGGMYDD ECPGAGMIAG IGRVSGREC VIVANDATVK GGTYYPITVK KHLRAQEIAL QNKLPCIYLV DSGGAFLPRQ DEVFPDRDHF GRIFYNQATM S AQGIAQIA AVLGSCTAGG AYVPAMSDEA VIVRNQGTIF LGGPPLVKAA TGEVVTAEEL GGGDLHSKTS GVTDHLAHDD RD ALRIVRN IVATLGPAEP PPWQVLPAVD PIADQTELYD VVPVDARVPY DVHEVITRIV DGGEFGEFKA EYGTTLVTGF ARI HGHPVG IIANNGVLFG ESAVKGAHFI ELCDKRKTPL LFLQNISGFM VGRDYEAGGI AKHGAKMVTA VACARVPKLT VVIG GSYGA GNYSMCGRAY SPRFLWMWPN ARISVMGGEQ AASVLATVRG EMTDAEAEEF KAPIREQYEH QGNPYYSTAR LWDDG VIDP ADTRTVVGLA LSVVGQAPLE PVSYGVFRM

UniProtKB: Carboxyl transferase domain protein

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Macromolecule #2: biotin carboxylase

MacromoleculeName: biotin carboxylase / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 70.144711 KDa
SequenceString: MMMSSQTFDT VLVANRGEIA VRVIRTLRAM GIRSVAVFSE ADAGARHVTE ADVAVCIGPA AARHSYLDID AVVGAARRTD AQAVHPGYG FLSENAEFAS ALATAGIVFI GPPASAIATM GDKIAAKAAV SAFGVPVVPG ISRPGLADDD LIAGAAEVGY P VLVKPSAG ...String:
MMMSSQTFDT VLVANRGEIA VRVIRTLRAM GIRSVAVFSE ADAGARHVTE ADVAVCIGPA AARHSYLDID AVVGAARRTD AQAVHPGYG FLSENAEFAS ALATAGIVFI GPPASAIATM GDKIAAKAAV SAFGVPVVPG ISRPGLADDD LIAGAAEVGY P VLVKPSAG GGGKGMRVVE AAADLPAALV SARREAGAAF GDDTLFLERF VQRPRHIEVQ VLADGHGNVI HLGERECSLQ RR HQKVIEE APSPLLDEAT RARIGAAACA TARSVDYTGA GTVEFIVSAD RPDEFFFMEM NTRLQVEHPV TELVTGIDLV EQQ IRIAAG EPLAIGQDDI TLTGHAVEAR VYAEDPAAGF LPTGGDVLGL REPTGRGVRV DSGLAAGTVV GSDYDPMLSK IIAH GSDRA SALQILDRAL ADTAVLGVTT NIEFLRFLLA DDDVAAGRLD TGLLDRRAPD FAPATVGDEQ LIAAAAYLWA RQWSA AGGD LWRVPSGWRV GEWAPATFRL HAGDRTDHVY ITGNPERASA AVEHGDTHTV SADFTPGSDT FAVTLDGLRT DYRVAV TDS QIWLSGGGRT WSVQKVREEP VRPDDAHSGD AELVSPMPGS VVAVGVPDGS DVTAGTVVVT VEAMKMEHAL TAPVDGV AK ILVAVGDQVK VGQPLARITA HTQENES

UniProtKB: biotin carboxylase

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Macromolecule #3: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 3 / Number of copies: 3 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12970
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: CryFold
Output model

PDB-31vx:
Cryo-EM structure of 3-methylcrotonyl-CoA carboxylase (MCC) complex (BC-engaged BCCP state)from Mycobacterium smegmatis

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