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Yorodumi- PDB-8f3d: 3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f3d | ||||||||||||||||||||||||
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Title | 3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered | ||||||||||||||||||||||||
Components |
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Keywords | LIGASE / enzyme / multienzyme / multi-enzyme / biotin-dependent / leucine catabolism / PROTEIN FIBRIL | ||||||||||||||||||||||||
Function / homology | Function and homology information urea carboxylase activity / propionyl-CoA carboxylase activity / methylcrotonoyl-CoA carboxylase activity / mitochondrion / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Leishmania tarentolae (eukaryote) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||||||||
Authors | Hu, J.J. / Lee, J.K.J. / Liu, Y.T. / Yu, C. / Huang, L. / Afasizheva, I. / Afasizhev, R. / Zhou, Z.H. | ||||||||||||||||||||||||
Funding support | United States, 7items
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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, J.J. / Lee, J.K.J. / Liu, Y.T. / Yu, C. / Huang, L. / Afasizheva, I. / Afasizhev, R. / Zhou, Z.H. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f3d.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8f3d.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8f3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f3d_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8f3d_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8f3d_validation.xml.gz | 220.4 KB | Display | |
Data in CIF | 8f3d_validation.cif.gz | 325.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/8f3d ftp://data.pdbj.org/pub/pdb/validation_reports/f3/8f3d | HTTPS FTP |
-Related structure data
Related structure data | 28846MC 8f41C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 76468.469 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: TATII/UC / References: methylcrotonoyl-CoA carboxylase #2: Protein | Mass: 76283.070 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: TATII/UC / References: UniProt: A0A640KPA4 #3: Chemical | ChemComp-BTI / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13250 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |