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- EMDB-50434: Pex5-Eci1 complex - Eci1 reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-50434
TitlePex5-Eci1 complex - Eci1 reconstruction
Map dataEci1-Pex5 complex sharpened map
Sample
  • Complex: Pex5-Eci1 complex
    • Protein or peptide: 3,2-trans-enoyl-CoA isomerase
KeywordsPeroxisome / protein targeting / PTS1 / PROTEIN TRANSPORT
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Peroxisomal protein import / fatty acid beta-oxidation / peroxisomal matrix / peroxisome
Similarity search - Function
: / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
3,2-trans-enoyl-CoA isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: 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, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50434.png

Downloads & links

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Map

FileDownload / File: emd_50434.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEci1-Pex5 complex sharpened map
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: 0.28
Minimum - Maximum-0.98506045 - 1.7587157
Average (Standard dev.)-0.0000026335597 (±0.03906871)
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_50434_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Eci1-Pex5 complex unfiltered map

Fileemd_50434_additional_1.map
AnnotationEci1-Pex5 complex unfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Eci1-Pex5 complex half map A

Fileemd_50434_half_map_1.map
AnnotationEci1-Pex5 complex half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Eci1-Pex5 complex half map B

Fileemd_50434_half_map_2.map
AnnotationEci1-Pex5 complex 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

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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: 6 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
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
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 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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