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Open data
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Basic information
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Title | Wild type hexamer oxalyl-CoA synthetase (OCS) | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | Lill P / Burgi J / Raunser S / Wilmanns M / Gatsogiannis C | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 4.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.7 KB 23.7 KB | Display Display | ![]() |
Images | ![]() | 39.7 KB | ||
Masks | ![]() | 23 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() ![]() | 1.7 MB 10.3 MB 12.1 MB 11.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8atdMC ![]() 8affC ![]() 8afgC 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
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
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-Additional map: #2
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-Additional map: #1
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-Half map: #2
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-Half map: #1
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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: ![]() ![]() ![]() |
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: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 48.135832 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 | ![]() |
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Aggregation state | particle |
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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. |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
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 |
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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![]() |