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- EMDB-28846: 3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered -
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Open data
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Basic information
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Title | 3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered | ||||||||||||||||||||||||
![]() | beta-subunit centered map | ||||||||||||||||||||||||
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![]() | enzyme / multienzyme / multi-enzyme / biotin-dependent / leucine catabolism / PROTEIN FIBRIL / LIGASE | ||||||||||||||||||||||||
Function / homology | ![]() urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / mitochondrion / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||||||||
![]() | Hu JJ / Lee JKJ / Liu YT / Yu C / Huang L / Afasizheva I / Afasizhev R / Zhou ZH | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 202 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 71.1 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 171.6 MB 171.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f3dMC ![]() 8f41C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | beta-subunit centered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half 1 of beta-subunit centered map
File | emd_28846_half_map_1.map | ||||||||||||
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Annotation | half 1 of beta-subunit centered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 2 of beta-subunit centered map
File | emd_28846_half_map_2.map | ||||||||||||
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Annotation | half 2 of beta-subunit centered map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
Entire | Name: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament |
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Components |
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-Supramolecule #1: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
Supramolecule | Name: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: 3-methylcrotonyl-CoA carboxylase beta-subunit
Macromolecule | Name: 3-methylcrotonyl-CoA carboxylase beta-subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: methylcrotonoyl-CoA carboxylase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 76.468469 KDa |
Sequence | String: 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 |
-Macromolecule #2: 3-methylcrotonyl-CoA carboxylase alpha-subunit
Macromolecule | Name: 3-methylcrotonyl-CoA carboxylase alpha-subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 76.28307 KDa |
Sequence | String: 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 |
-Macromolecule #3: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Macromolecule | Name: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL type: ligand / ID: 3 / Number of copies: 6 / Formula: BTI |
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Molecular weight | Theoretical: 228.311 Da |
Chemical component information | ![]() ChemComp-BTI: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8f3d: |