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- EMDB-56149: L. pneumophila 3-methylcrotonyl-CoA carboxylase A1B6 -

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Basic information

Entry
Database: EMDB / ID: EMD-56149
TitleL. pneumophila 3-methylcrotonyl-CoA carboxylase A1B6
Map dataL. pneumophila 3-methylcrotonyl-CoA carboxylase A1B6
Sample
  • Complex: L. pneumophila 3-methylcrotonyl-CoA carboxylase
    • Protein or peptide: Propionyl CoA carboxylase beta subunit
    • Protein or peptide: Biotin carboxylase
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Keywords3-methylcrotonyl-CoA carboxylase / ligase / biotin
Function / homology
Function and homology information


methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase / L-leucine catabolic process / propionyl-CoA carboxylase activity / ligase activity / ATP binding / metal ion binding
Similarity search - Function
Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. ...Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 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 / Propionyl CoA carboxylase beta subunit
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsMeir A / Durie C / Somarathne R / Shrestha R / Zehra M / Brodeur C / Bhella D / Lai WC
Funding support United States, United Kingdom, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150663 United States
Medical Research Council (MRC, United Kingdom)MC_UU_00034/1 United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Substrate-enhanced filamentation of 3-methylcrotonyl-CoA carboxylase in .
Authors: Radha P Somarathne / Riti Shrestha / Mishghan Zehra / Cole Brodeur / David Bhella / Wing-Cheung Lai / Amit Meir / Clarissa L Durie
Abstract: 3-Methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent carboxylase that metabolizes the amino acid leucine. MCC is present in bacteria, fungi, plants, and animals. In humans, its overexpression ...3-Methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent carboxylase that metabolizes the amino acid leucine. MCC is present in bacteria, fungi, plants, and animals. In humans, its overexpression is linked to cancer, and its deficiency is linked to inborn errors of metabolism with severe consequences, so understanding its structure and function has far reaching implications. Here, we explore the MCC from , a pathogenic bacterium with a biphasic life cycle. Our endogenous holoenzyme yielded the highest resolution cryo-EM structure of MCC to date, allowing for identification of protein components by the machine learning tool ModelAngelo, confirmed independently by mass spectrometry. We also observed, for the first time, enhanced filamentation of MCC upon substrate binding. We propose that this filamentation, previously observed in the eukaryotes, but not in bacteria, may be important for cellular processes such as differentiation of life cycle or cell division.
History
DepositionDec 22, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56149.png

Downloads & links

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Map

FileDownload / File: emd_56149.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationL. pneumophila 3-methylcrotonyl-CoA carboxylase A1B6
Voxel sizeX=Y=Z: 0.75 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.80280787 - 1.222305
Average (Standard dev.)-0.00002104006 (±0.031745378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_56149_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_56149_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 : L. pneumophila 3-methylcrotonyl-CoA carboxylase

EntireName: L. pneumophila 3-methylcrotonyl-CoA carboxylase
Components
  • Complex: L. pneumophila 3-methylcrotonyl-CoA carboxylase
    • Protein or peptide: Propionyl CoA carboxylase beta subunit
    • Protein or peptide: Biotin carboxylase
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: L. pneumophila 3-methylcrotonyl-CoA carboxylase

SupramoleculeName: L. pneumophila 3-methylcrotonyl-CoA carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Location in cell: Cytoplasm
Molecular weightTheoretical: 365 kDa/nm

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Macromolecule #1: Propionyl CoA carboxylase beta subunit

MacromoleculeName: Propionyl CoA carboxylase beta subunit / type: protein_or_peptide / ID: 1 / Details: lpg1827 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Legionella pneumophila (bacteria) / Strain: Phildelphia 1
Molecular weightTheoretical: 58.525625 KDa
SequenceString: MAKLTTQINT SSQEFKNNQA NMQALVTDLR EKIHQISLGG DEKARTKHQQ QGKLLPRERL HQLLDPGSPF LELSQLAAYQ VYEDTIPAA GIITGIGRVA GNECVIVVND ATVKGGTYYP LTVKKHLRAQ EIALINHLPC IYLVDSGGAF LPLQDQVFAD K EHFGRVFY ...String:
MAKLTTQINT SSQEFKNNQA NMQALVTDLR EKIHQISLGG DEKARTKHQQ QGKLLPRERL HQLLDPGSPF LELSQLAAYQ VYEDTIPAA GIITGIGRVA GNECVIVVND ATVKGGTYYP LTVKKHLRAQ EIALINHLPC IYLVDSGGAF LPLQDQVFAD K EHFGRVFY NQAQMSALNI PQIAVVMGSC TAGGAYVPAM ADESIMVKNQ ATIFLGGPPL VKAATGEVIS AEELGGAEVH CR HSGVSDH YAENDAHALH LARVAISNLN RKKPDSIHRV DTVPPLYDSE DLTGIIPTDP RKPFDIREII ARVVDGSEFD EFK ALFGTT LVCGFARLYG YPIGIIANNG ILFSESAQKG SHFIELCCQR KIPLVFLQNI TGFMVGSKYE ASGIAKHGAK MVTA VANAN VPKFTIIVGG SFGAGNYAMC GRAYAPRFLW AWPNARISVM GGEQAANVLA QITREKYAKQ GKEWSLEEEE QFKTQ MRSQ YETQGNPYYA SARLWDDGVI APQDTRKILG LGLSAALNAP IEDTRFGVFR M

UniProtKB: Propionyl CoA carboxylase beta subunit

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Macromolecule #2: Biotin carboxylase

MacromoleculeName: Biotin carboxylase / type: protein_or_peptide / ID: 2 / Details: lpg 1829 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria) / Strain: Philadelphia 1
Molecular weightTheoretical: 75.810953 KDa
SequenceString: MRGKKGLKHF SIKKYPTGIK VLDMFNKILI ANRGEIACRI IKTAHSMGIQ AIAVYSAADR NSLHVRLADS AYYIGEAPAK ESYLNIDHI IQAAKESGAQ AIHPGYGFLS ENPDFAKACE QAGIVFIGPS IKAMEAMASK QLAKQLLEKT KVPLTPGYHG V EQSEEKLL ...String:
MRGKKGLKHF SIKKYPTGIK VLDMFNKILI ANRGEIACRI IKTAHSMGIQ AIAVYSAADR NSLHVRLADS AYYIGEAPAK ESYLNIDHI IQAAKESGAQ AIHPGYGFLS ENPDFAKACE QAGIVFIGPS IKAMEAMASK QLAKQLLEKT KVPLTPGYHG V EQSEEKLL SEAKKIGFPV LIKAANGGGG KGMRAVHDEK EFHDALAGAK RESMASFADD TMIIERLVLN PRHVEVQIMA DN HGNVVNL FERDCSIQRR HQKIIEEAPA PNLLPVLRQR LAEAACEVAR SINYRGAGTV EFLVDGEDKF YFMEMNTRLQ VEH PVTEMI TGLDLVAWQI KIAANDTLPL LQNQIQAQGH AIECRIYAED PYQGFIPSIG QLQFLKEPSG DGIRIDTGVT LSSE ITRYY DPMIAKLIAW GHNREEALHR LERSLAHYDI GGVKTNIPFL RAICQHVKFK EAKLSTDFLE KENISLPKPD NELGM LLAI SYDYLGMINR TTDPLLQEAF GWQMHLSSHW IWRYQLNSTI IEAQITPIDN KKFKAKIENK EMVIYARYDI DQLIIE IDQ KSVKARVENK DHHLIFYTDK GQLSIERFYW SKLDAQTSAH KGQLTAPMPA TVVAILKNIG EQVKAGESLI VLEAMKM EH TIHAPIDGIL SDIFYSVGSQ VSEGAELLAL SESDT

UniProtKB: Biotin carboxylase

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Macromolecule #3: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

MacromoleculeName: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
type: ligand / ID: 3 / Number of copies: 3 / Formula: BTI
Molecular weightTheoretical: 228.311 Da
Chemical component information

ChemComp-BTI:
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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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

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
SoftwareName: EPU / Details: EPU was used for data collection
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 31641 / Average exposure time: 3.22 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1504197
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 78376
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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