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- EMDB-50435: Pex5-Eci1 complex - Pex5 local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-50435
TitlePex5-Eci1 complex - Pex5 local refinement
Map dataPex5 local refinement
Sample
  • Complex: Pex5-Eci1 complex
    • Protein or peptide: 3,2-trans-enoyl-CoA isomerase
    • Protein or peptide: Peroxisomal targeting signal receptor
KeywordsPeroxisome / protein targeting / PTS1 / PROTEIN TRANSPORT
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 / : / peroxisomal membrane / fatty acid beta-oxidation / peroxisomal matrix / peroxisome / protein-macromolecule adaptor activity / cytosol
Similarity search - Function
PEX5/PEX5L / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Tetratricopeptide repeat / Tetratricopeptide repeat / ClpP/crotonase-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...PEX5/PEX5L / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Tetratricopeptide repeat / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsElad N / Dym O
Funding supportEuropean Union, Israel, 2 items
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, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50435.png

Downloads & links

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Map

FileDownload / File: emd_50435.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPex5 local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336.8 Å		0.84 Å/pix.
x 400 pix.
= 336.8 Å		0.84 Å/pix.
x 400 pix.
= 336.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.62994295 - 1.1483415
Average (Standard dev.)0.00009512036 (±0.022856915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50435_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Pex5 local refinement unfiltered map

Fileemd_50435_additional_1.map
AnnotationPex5 local refinement unfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pex5 local refinement half map A

Fileemd_50435_half_map_1.map
AnnotationPex5 local refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pex5 local refinement half map B

Fileemd_50435_half_map_2.map
AnnotationPex5 local refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pex5-Eci1 complex

EntireName: Pex5-Eci1 complex
Components
  • Complex: Pex5-Eci1 complex
    • Protein or peptide: 3,2-trans-enoyl-CoA isomerase
    • Protein or peptide: Peroxisomal targeting signal receptor

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Supramolecule #1: Pex5-Eci1 complex

SupramoleculeName: Pex5-Eci1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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

MacromoleculeName: 3,2-trans-enoyl-CoA isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.736408 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQEIRQNEK ISYRIEGPFF IIHLMNPDNL NALEGEDYIY LGELLELADR NRDVYFTIIQ SSGRFFSSGA DFKGIAKAQG DDTNKYPSE TSKWVSNFVA RNVYVTDAFI KHSKVLICCL NGPAIGLSAA LVALCDIVYS INDKVYLLYP FANLGLITEG G TTVSLPLK ...String:
MSQEIRQNEK ISYRIEGPFF IIHLMNPDNL NALEGEDYIY LGELLELADR NRDVYFTIIQ SSGRFFSSGA DFKGIAKAQG DDTNKYPSE TSKWVSNFVA RNVYVTDAFI KHSKVLICCL NGPAIGLSAA LVALCDIVYS INDKVYLLYP FANLGLITEG G TTVSLPLK FGTNTTYECL MFNKPFKYDI MCENGFISKN FNMPSSNAEA FNAKVLEELR EKVKGLYLPS CLGMKKLLKS NH IDAFNKA NSVEVNESLK YWVDGEPLKR FRQLGSKQRK HRL

UniProtKB: 3,2-trans-enoyl-CoA isomerase

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Macromolecule #2: Peroxisomal targeting signal receptor

MacromoleculeName: Peroxisomal targeting signal receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 69.335766 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: ADVGSCSVGN NPLAQLHKHT QQNKSLQFNQ KNNGRLNESP LQGTNKPGIS EAFISNVNAI SQENMANMQR FINGEPLIDD KRRMEIGPS SGRLPPFSNV HSLQTSANPT QIKGVNDISH WSQEFQGSNS IQNRNADTGN SEKAWQRGST TASSRFQYPN T MMNNYAYA ...String:
ADVGSCSVGN NPLAQLHKHT QQNKSLQFNQ KNNGRLNESP LQGTNKPGIS EAFISNVNAI SQENMANMQR FINGEPLIDD KRRMEIGPS SGRLPPFSNV HSLQTSANPT QIKGVNDISH WSQEFQGSNS IQNRNADTGN SEKAWQRGST TASSRFQYPN T MMNNYAYA SMNSLSGSRL QSPAFMNQQQ SGRSKEGVNE QEQQPWTDQF EKLEKEVSEN LDINDEIEKE ENVSEVEQNK PE TVEKEEG VYGDQYQSDF QEVWDSIHKD AEEVLPSELV NDDLNLGEDY LKYLGGRVNG NIEYAFQSNN EYFNNPNAYK IGC LLMENG AKLSEAALAF EAAVKEKPDH VDAWLRLGLV QTQNEKELNG ISALEECLKL DPKNLEAMKT LAISYINEGY DMSA FTMLD KWAETKYPEI WSRIKQQDDK FQKEKGFTHI DMNAHITKQF LQLANNLSTI DPEIQLCLGL LFYTKDDFDK TIDCF ESAL RVNPNDELMW NRLGASLANS NRSEEAIQAY HRALQLKPSF VRARYNLAVS SMNIGCFKEA AGYLLSVLSM HEVNTN NKK GDVGSLLNTY NDTVIETLKR VFIAMNRDDL LQEVKPGMDL KRFKGEFSF

UniProtKB: Peroxisomal targeting signal receptor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5577 / Average exposure time: 1.6 sec. / Average electron dose: 45.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 59382 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 15.0 µm / Nominal defocus min: 2.7 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

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Image processing

Particle selectionNumber selected: 2170575
CTF correctionSoftware - Name: cryoSPARC (ver. 3.0.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117945
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC / Details: The map is from one class out of 10
FSC plot (resolution estimation)

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