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Open data
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Basic information
Entry | Database: PDB / ID: 8sgy | |||||||||
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Title | Leishmania tarentolae propionyl-CoA carboxylase (alpha-5-beta-6) | |||||||||
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![]() | LIGASE / Multienzyme complex / carboxylase | |||||||||
Function / homology | ![]() propionyl-CoA carboxylase / urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / lipid catabolic process / mitochondrion / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.62 Å | |||||||||
![]() | Lee, J.K.J. / Liu, Y.T. / Hu, J.J. / Aphasizheva, I. / Aphasizhev, R. / Zhou, Z.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics. Authors: Jane K J Lee / Yun-Tao Liu / Jason J Hu / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou / ![]() Abstract: Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present ...Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoan (LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC β-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulae αβ, αβ, αβ, αβ, αβ, αβ, αβ) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1014.1 KB | Display | ![]() |
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PDB format | ![]() | 855.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 175.1 KB | Display | |
Data in CIF | ![]() | 255.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40473MC ![]() 8sgxC ![]() 8sgzC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 73277.656 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 53587.285 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #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: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Leishmania tarentolae propionyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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Processing
Software | Name: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package |
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EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement |
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 8.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16034 / Symmetry type: POINT |