[English] 日本語
Yorodumi
- EMDB-15646: Wild type hexamer oxalyl-CoA synthetase (OCS) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15646
TitleWild type hexamer oxalyl-CoA synthetase (OCS)
Map data
Sample
  • Complex: Hexameric complex of the oxalyl-CoA synthetase Pcs60p
    • Protein or peptide: Oxalate--CoA ligase
KeywordsPeroxisome / Oxalyl-CoA ligase / Oligomer / Yeast / LIGASE
Function / homology
Function and homology information


oxalate-CoA ligase / oxalate-CoA ligase activity / oxalate catabolic process / medium-chain fatty acid-CoA ligase activity / peroxisomal membrane / peroxisomal matrix / fatty acid metabolic process / mRNA binding / ATP binding / cytoplasm
Similarity search - Function
Oxalate--CoA ligase Pcs60-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLill P / Burgi J / Raunser S / Wilmanns M / Gatsogiannis C
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)MW 1058/9-1 Germany
German Research Foundation (DFG)MW 1058/9-2 Germany
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
German Research Foundation (DFG)GA 2519/1-2 Germany
German Research Foundation (DFG)RA 1781/4-2 Germany
CitationJournal: 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
DepositionAug 23, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15646.png

Downloads & links

-
Map

FileDownload / File: emd_15646.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 182 pix.
= 198.38 Å		1.09 Å/pix.
x 182 pix.
= 198.38 Å		1.09 Å/pix.
x 182 pix.
= 198.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.12420904 - 0.2280988
Average (Standard dev.)0.00044296868 (±0.008846786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions182182182
Spacing182182182
CellA=B=C: 198.38 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15646_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_15646_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_15646_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15646_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15646_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Hexameric complex of the oxalyl-CoA synthetase Pcs60p

EntireName: Hexameric complex of the oxalyl-CoA synthetase Pcs60p
Components
  • Complex: Hexameric complex of the oxalyl-CoA synthetase Pcs60p
    • Protein or peptide: Oxalate--CoA ligase

-
Supramolecule #1: Hexameric complex of the oxalyl-CoA synthetase Pcs60p

SupramoleculeName: Hexameric complex of the oxalyl-CoA synthetase Pcs60p / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 360 KDa

-
Macromolecule #1: Oxalate--CoA ligase

MacromoleculeName: Oxalate--CoA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: oxalate-CoA ligase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 48.135832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHepes
150.0 mMNaClSodium chloride
0.5 mMC9H15O6PTCEP
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen 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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.2 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4000000 / Details: Picking was performed using cryOLO
Startup modelType of model: INSILICO MODEL
In silico model: Initial model was computed from 2D classes using VIPER (SPHIRE Package)
Final reconstructionApplied 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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.2) / Software - details: VIPER
Final angle assignmentType: OTHER / Software - Name: SPHIRE (ver. 1.3) / Software - details: Meridien

-
Atomic model buiding 1

Initial modelPDB ID:

8aff


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8atd:
Wild type hexamer oxalyl-CoA synthetase (OCS)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more