+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15646 | ||||||||||||||||||
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Title | Wild type hexamer oxalyl-CoA synthetase (OCS) | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Peroxisome / Oxalyl-CoA ligase / Oligomer / Yeast / LIGASE | ||||||||||||||||||
Function / homology | Function and homology information oxalate-CoA ligase / medium-chain fatty acid-CoA ligase activity / oxalate-CoA ligase activity / oxalate catabolic process / peroxisomal membrane / peroxisomal matrix / fatty acid metabolic process / mRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Lill P / Burgi J / Raunser S / Wilmanns M / Gatsogiannis C | ||||||||||||||||||
Funding support | Germany, 5 items
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Citation | Journal: Biol Chem / Year: 2023 Title: Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase. Authors: Jérôme Bürgi / Pascal Lill / Evdokia-Anastasia Giannopoulou / Cy M Jeffries / Grzegorz Chojnowski / Stefan Raunser / Christos Gatsogiannis / Matthias Wilmanns / Abstract: Oxalyl-CoA synthetase from is one of the most abundant peroxisomal proteins in yeast and hence has become a model to study peroxisomal translocation. It contains a C-terminal Peroxisome Targeting ...Oxalyl-CoA synthetase from is one of the most abundant peroxisomal proteins in yeast and hence has become a model to study peroxisomal translocation. It contains a C-terminal Peroxisome Targeting Signal 1, which however is partly dispensable, suggesting additional receptor bindings sites. To unravel any additional features that may contribute to its capacity to be recognized as peroxisomal target, we determined its assembly and overall architecture by an integrated structural biology approach, including X-ray crystallography, single particle cryo-electron microscopy and small angle X-ray scattering. Surprisingly, it assembles into mixture of concentration-dependent dimers, tetramers and hexamers by dimer self-association. Hexameric particles form an unprecedented asymmetric horseshoe-like arrangement, which considerably differs from symmetric hexameric assembly found in many other protein structures. A single mutation within the self-association interface is sufficient to abolish any higher-level oligomerization, resulting in a homogenous dimeric assembly. The small C-terminal domain of yeast Oxalyl-CoA synthetase is connected by a partly flexible hinge with the large N-terminal domain, which provides the sole basis for oligomeric assembly. Our data provide a basis to mechanistically study peroxisomal translocation of this target. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15646.map.gz | 4.5 MB | EMDB map data format | |
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Header (meta data) | emd-15646-v30.xml emd-15646.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
Images | emd_15646.png | 39.7 KB | ||
Masks | emd_15646_msk_1.map | 23 MB | Mask map | |
Filedesc metadata | emd-15646.cif.gz | 6.7 KB | ||
Others | emd_15646_additional_1.map.gz emd_15646_additional_2.map.gz emd_15646_half_map_1.map.gz emd_15646_half_map_2.map.gz | 1.7 MB 10.3 MB 12.1 MB 11.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15646 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15646 | HTTPS FTP |
-Related structure data
Related structure data | 8atdMC 8affC 8afgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15646.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15646_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_15646_additional_1.map | ||||||||||||
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-Additional map: #1
File | emd_15646_additional_2.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_15646_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_15646_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hexameric complex of the oxalyl-CoA synthetase Pcs60p
Entire | Name: Hexameric complex of the oxalyl-CoA synthetase Pcs60p |
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Components |
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-Supramolecule #1: Hexameric complex of the oxalyl-CoA synthetase Pcs60p
Supramolecule | Name: Hexameric complex of the oxalyl-CoA synthetase Pcs60p / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 360 KDa |
-Macromolecule #1: Oxalate--CoA ligase
Macromolecule | Name: Oxalate--CoA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: oxalate-CoA ligase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 48.135832 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TVTASFNDTF SVSDNVAVIV PETDTQVTYR DLSHMVGHFQ TMFTNPNSPL YGAVFRQDTV AISMRNGLEF IVAFLGATMD AKIGAPLNP NYKEKEFNFY LNDLKSKAIC VPKGTTKLQS SEILKSASTF GCFIVELAFD ATRFRVEYDI YSPEDNYKRV I YRSLNNAK ...String: TVTASFNDTF SVSDNVAVIV PETDTQVTYR DLSHMVGHFQ TMFTNPNSPL YGAVFRQDTV AISMRNGLEF IVAFLGATMD AKIGAPLNP NYKEKEFNFY LNDLKSKAIC VPKGTTKLQS SEILKSASTF GCFIVELAFD ATRFRVEYDI YSPEDNYKRV I YRSLNNAK FVNTNPVKFP GFARSSDVAL ILHTSGTTST PKTVPLLHLN IVRSTLNIAN TYKLTPLDRS YVVMPLFHVH GL IGVLLST FRTQGSVVVP DGFHPKLFWD QFVKYNCNWF SCVPTISMIM LNMPKPNPFP HIRFIRSCSS ALAPATFHKL EKE FNAPVL EAYAMTEASH QMTSNNLPPG KRKPGTVGQP QGVTVVILDD NDNVLPPGKV GEVSIRGENV TLGYANNPKA NKEN FTKRE NYFRTGDQGY FDPEGFLVLT GRIKEL UniProtKB: Oxalate--CoA ligase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298.15 K / Instrument: GATAN CRYOPLUNGE 3 Details: 90% humidity in the sample chamber. Gentle Blot function, 2.5 seconds. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-60 / Number grids imaged: 4 / Number real images: 5594 / Average electron dose: 63.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 4000000 / Details: Picking was performed using cryOLO |
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Startup model | Type of model: INSILICO MODEL In silico model: Initial model was computed from 2D classes using VIPER (SPHIRE Package) |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.2) / Software - details: VIPER |
Final angle assignment | Type: OTHER / Software - Name: SPHIRE (ver. 1.3) / Software - details: Meridien |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.3) / Software - details: Post Refinement / Number images used: 819000 |