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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: J Cell Sci / Year: 2025
Title: A cryo-electron microscopy structure of yeast Pex5 in complex with a cargo uncovers a novel binding interface.
Authors: Lior Peer / Orly Dym / Nadav Elad / Asa Tirosh / Jossef Jacobovitch / Ehud Sivan / Mor Angel / Shira Albeck / Maya Schuldiner / Yoav Peleg / Einat Zalckvar /
Abstract: Proper protein targeting to organelles is crucial for maintaining eukaryotic cellular function and homeostasis. This necessity has driven the evolution of specific targeting signals on proteins and ...Proper protein targeting to organelles is crucial for maintaining eukaryotic cellular function and homeostasis. This necessity has driven the evolution of specific targeting signals on proteins and the targeting factors that recognize them. A prominent example is peroxisomal matrix proteins, most of which depend on the targeting factor Pex5 to localize and function correctly. Although most Pex5 cargoes contain a peroxisomal targeting signal type 1 (PTS1), they are not all targeted similarly. Some undergo priority targeting, facilitated either by stronger binding to specific subsets of PTS1 signals or by additional interaction interfaces. These observations highlight the extensive complexity of Pex5-mediated targeting. In this study, we reveal that the Saccharomyces cerevisiae (yeast) matrix protein Eci1 can reach peroxisomes and bind Pex5 in the absence of PTS1. By solving the structure of the yeast Pex5-Eci1 complex using cryo-electron microscopy, we identified additional binding interfaces. Our findings provide new insights into the versatile interactions between Pex5 and its cargo, Eci1. More broadly, this work highlights the intricate, dynamic nature of the interactions between cargo factors and their cargoes to meet the complex environment within eukaryotic cells.
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
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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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