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- EMDB-40055: Focused map of Pex region of Trypanosoma docking complex, (MDH)4-... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-40055
TitleFocused map of Pex region of Trypanosoma docking complex, (MDH)4-(Pex5)1-(Pex14)1
Map data
Sample
  • Complex: Complex of MDH-tetramer and PEX5
KeywordsPeroxisomal transport / Import / PEX / TRANSPORT PROTEIN
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSonani RR / Artur B / Jemiola-Rzeminska M / Lipinski O / Patel SN / Sood T / Dubin G
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2020/39/B/NZ1/01551 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: To Be Published
Title: Structure of Trypanosoma MDH4-Pex5, close conformation
Authors: Sonani RR / Dubin G
History
DepositionMar 13, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40055.png

Downloads & links

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Map

FileDownload / File: emd_40055.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.347877 - 3.7117522
Average (Standard dev.)-0.00030634762 (±0.027558807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40055_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40055_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40055_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of MDH-tetramer and PEX5

EntireName: Complex of MDH-tetramer and PEX5
Components
  • Complex: Complex of MDH-tetramer and PEX5

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Supramolecule #1: Complex of MDH-tetramer and PEX5

SupramoleculeName: Complex of MDH-tetramer and PEX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92486
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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