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- PDB-9fh0: Pex5-Eci1 complex - Pex5 local refinement -

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Basic information

Entry
Database: PDB / ID: 9fh0
TitlePex5-Eci1 complex - Pex5 local refinement
Components
  • 3,2-trans-enoyl-CoA isomerase
  • Peroxisomal targeting signal receptor
KeywordsPROTEIN TRANSPORT / Peroxisome / protein targeting / PTS1
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / peroxisome matrix targeting signal-1 binding / Pexophagy / peroxisomal importomer complex / protein import into peroxisome matrix / Delta3-Delta2-enoyl-CoA isomerase / protein import into peroxisome matrix, docking / delta(3)-delta(2)-enoyl-CoA isomerase activity / Peroxisomal protein import / protein carrier chaperone ...Beta-oxidation of very long chain fatty acids / peroxisome matrix targeting signal-1 binding / Pexophagy / peroxisomal importomer complex / protein import into peroxisome matrix / Delta3-Delta2-enoyl-CoA isomerase / protein import into peroxisome matrix, docking / delta(3)-delta(2)-enoyl-CoA isomerase activity / Peroxisomal protein import / protein carrier chaperone / E3 ubiquitin ligases ubiquitinate target proteins / peroxisomal membrane / fatty acid beta-oxidation / peroxisomal matrix / peroxisome / protein-macromolecule adaptor activity / cytosol
Similarity search - Function
PEX5/PEX5L / : / Tetratricopeptide repeat / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Tetratricopeptide repeat / ClpP/crotonase-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...PEX5/PEX5L / : / Tetratricopeptide repeat / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Tetratricopeptide repeat / ClpP/crotonase-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Peroxisomal targeting signal receptor / 3,2-trans-enoyl-CoA isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsElad, N. / Dym, O.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)864068European Union
Israel Science Foundation760/17 Israel
CitationJournal: To Be Published
Title: An unconventional interaction interface between the peroxisomal targeting factor Pex5 and Eci1 enables PTS1 independent import
Authors: Peer, L. / Elad, N. / Dym, O. / Tirosh, A. / Jacobovitch, J. / Albeck, S. / Schuldiner, M. / Peleg, Y. / Zalckvar, E.
History
DepositionMay 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,2-trans-enoyl-CoA isomerase
G: Peroxisomal targeting signal receptor


Theoretical massNumber of molelcules
Total (without water)101,0722
Polymers101,0722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, This entry include the coordinate of Pex5 and one out of 6 copies of Eci1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 3,2-trans-enoyl-CoA isomerase


Mass: 31736.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ECI1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05871
#2: Protein Peroxisomal targeting signal receptor / PTS1 receptor / PTS1R / Peroxin-5


Mass: 69335.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PEX5, PAS10, YDR244W, YD8419.11 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P35056
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pex5-Eci1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 59382 X / Nominal defocus max: 15000 nm / Nominal defocus min: 2700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 45.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5577
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC3.0.1particle selection
2PHENIX1.15.2_3472:model refinement
3SerialEM3.9image acquisitionbeta-7
5cryoSPARC3.0.1CTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2170575
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117945 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0134592
ELECTRON MICROSCOPYf_angle_d0.8046216
ELECTRON MICROSCOPYf_dihedral_angle_d7.5592748
ELECTRON MICROSCOPYf_chiral_restr0.055701
ELECTRON MICROSCOPYf_plane_restr0.005797

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