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- EMDB-28846: 3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered -

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Basic information

Entry
Database: EMDB / ID: EMD-28846
Title3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered
Map databeta-subunit centered map
Sample
  • Complex: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase beta-subunit
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase alpha-subunit
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Keywordsenzyme / multienzyme / multi-enzyme / biotin-dependent / leucine catabolism / PROTEIN FIBRIL / LIGASE
Function / homology
Function and homology information


methylcrotonoyl-CoA carboxylase activity / mitochondrion / ATP binding / metal ion binding / membrane
Similarity search - Function
: / 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 ...: / 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 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. / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Methylcrotonoyl-coa carboxylase biotinylated subunitprotein-like protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHu JJ / Lee JKJ / Liu YT / Yu C / Huang L / Afasizheva I / Afasizhev R / Zhou ZH
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM074830 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Science Foundation (NSF, United States)DBI-133813 United States
Citation
Journal: Structure / Year: 2023
Title: Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase.
Authors: Jason J Hu / Jane K J Lee / Yun-Tao Liu / Clinton Yu / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: 3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been ...3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. αβ LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking αβ LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
#1: Journal: To Be Published
Title: Discovery, Structure, and Function of Filamentous 3-Methylcrotonyl-CoA Carboxylase
Authors: Hu JJ / Lee JKJ / Liu YT / Yu C / Huang L / Afasizheva I / Afasizhev R / Zhou ZH
History
DepositionNov 9, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28846.png

Downloads & links

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Map

FileDownload / File: emd_28846.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbeta-subunit centered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.063955285 - 0.08914003
Average (Standard dev.)0.00014838424 (±0.0044202683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 1 of beta-subunit centered map

Fileemd_28846_half_map_1.map
Annotationhalf 1 of beta-subunit centered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 of beta-subunit centered map

Fileemd_28846_half_map_2.map
Annotationhalf 2 of beta-subunit centered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament

EntireName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
Components
  • Complex: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase beta-subunit
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase alpha-subunit
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament

SupramoleculeName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC

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Macromolecule #1: 3-methylcrotonyl-CoA carboxylase beta-subunit

MacromoleculeName: 3-methylcrotonyl-CoA carboxylase beta-subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: methylcrotonoyl-CoA carboxylase
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC
Molecular weightTheoretical: 76.468469 KDa
SequenceString: MDKTHVLRNT TRGMFRTSMM RVLGRPGSLS VTASAGGTAC VPMAALLRRS ATPAAASATA ASAMSALWCT RCFESSSAGS PPKVSDAGM KERSTQEPCV AATPTPSDTA ATLAAAATPA PAAPIKSKGV DYARLYAHHP IDYERSTSKS PNILRLPANT S DPTYQENM ...String:
MDKTHVLRNT TRGMFRTSMM RVLGRPGSLS VTASAGGTAC VPMAALLRRS ATPAAASATA ASAMSALWCT RCFESSSAGS PPKVSDAGM KERSTQEPCV AATPTPSDTA ATLAAAATPA PAAPIKSKGV DYARLYAHHP IDYERSTSKS PNILRLPANT S DPTYQENM ARMEGLVEQL RARVRYVQAG GVVPEEEAAK AGVSISSIEA DDRVRKLHLS RGKMLARDRI ERLIDPGTRF LE LSQLAGW DLYWDDKKKE YERCYSGGIV TGIGLVNGVR CMLVANDATV KGGTYYPITV KKHLRAQKIA EQNHLPCIYL VDS GGANLS RQDDVFPDEQ HFGRIFYNEA QMSIKSISQI AVVMGSCTAG GAYVPAMADE NIIVARNGTI FLGGPPLVLA ATGE KVSSE ELGGADVHCR ISGVGDHYAT DDLHALYLAR RAVANLNLKE HNEARNPTDV KPVPPLYDPR ELGGFIPDML SDVVK SFDV RAIIARIVDG SRFDEFKALY GNTLVCGFAR IEGMQVGIIA NQGILYSESA LKGAHFIGLC TQRNVPLLFL QNITGF MVG KKYEEGGIAR NGARLVMAVS SAPVPKVTVL IGGSYGAGNY GMCGRAFEPR FLFMWPNARI SVMGGTQAAT VLTLTNR NL KNASEAEIAA FKDKVKKKYE KEGSCYYSTA RLWDDGVIAP EDTRVVVAEA LRATRLAPME KRERV

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Macromolecule #2: 3-methylcrotonyl-CoA carboxylase alpha-subunit

MacromoleculeName: 3-methylcrotonyl-CoA carboxylase alpha-subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC
Molecular weightTheoretical: 76.28307 KDa
SequenceString: MLRYTGLWRE RKVEKLLVAN RGEIACRVFR TCREMHIRTV ALFCEAERNA KHVAEADEAV CIGPPPAVNS YLRGEHIISV AKQLNVDAI HPGYGFLSEN ASFADAITRS GIEFIGPPAS AISLMGSKSE SKRIMEAAGV PVVPGYYGEN QNVSFLAEEA K KVGFPILI ...String:
MLRYTGLWRE RKVEKLLVAN RGEIACRVFR TCREMHIRTV ALFCEAERNA KHVAEADEAV CIGPPPAVNS YLRGEHIISV AKQLNVDAI HPGYGFLSEN ASFADAITRS GIEFIGPPAS AISLMGSKSE SKRIMEAAGV PVVPGYYGEN QNVSFLAEEA K KVGFPILI KAVSGGGGKG MKIVERPEDF TFMLESAKRE ATNFFKDDRV ILERYVKRSR HIECQIFFDK HGRGVFFFER DC SVQRRYQ KVLEEAPAPH LSMETRQRIG EVALQAAKAV GYVGAGTVEF IFDTSTGEFY FMEMNTRLQV EHPVTEEVCR IKG APLDLV KLQIKTAMGK PLTFSQEDVT LVGSCIEARV YAESPERGFL PESGPLTFIR EPFQGVRGPA RTRLDTGFRE GDNV LIHYD PMLAKVISWG RSREEALRGL RQALGEYKVA GINTNIEFLK RCCETPEFAR GGVTTNFISE HESQLLKSPV VTPEV AAMA ATAWLLNRCD NWRGAFRLNS DTNATVHFYI DDHPVEVRLH TEGANYHKIF FSVWDHDGSF EVCSGPVTSK HRDQKS IVN DFTFLFENGM HHTVLAVATE GDVTVIGSFG LHQLRLLPLT DGFGDSSTAG GTSTKIVSPM PGKVSKLLVK SGDLVEK GQ VLVIVEAMKM EHPVRALQDG RVSFLVKEGE VVGGDHVLAT VAEEE

UniProtKB: Methylcrotonoyl-coa carboxylase biotinylated subunitprotein-like protein

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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: 6 / 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 statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13250
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8f3d:
3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered

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