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- EMDB-40053: Consensus cryo-EM reconstruction of Trypanosoma Docking complex -

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Basic information

Entry
Database: EMDB / ID: EMD-40053
TitleConsensus cryo-EM reconstruction of Trypanosoma Docking complex
Map data
Sample
  • Complex: MDH-tetramer in docking complex (MDH)4-(Pex5)1-(Pex14)1
    • Protein or peptide: MDH tetramer in docking complex
KeywordsPeroxisomal transport / Import / PEX / TRANSPORT PROTEIN / PROTEIN TRANSPORT
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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: Focused map of MDH-tetramer in Trypanosoma docking complex
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_40053.png

Downloads & links

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Map

FileDownload / File: emd_40053.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: 0.4
Minimum - Maximum-1.5946001 - 2.2495859
Average (Standard dev.)-0.0003216798 (±0.044545338)
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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Half map: #1

Fileemd_40053_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40053_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 : MDH-tetramer in docking complex (MDH)4-(Pex5)1-(Pex14)1

EntireName: MDH-tetramer in docking complex (MDH)4-(Pex5)1-(Pex14)1
Components
  • Complex: MDH-tetramer in docking complex (MDH)4-(Pex5)1-(Pex14)1
    • Protein or peptide: MDH tetramer in docking complex

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Supramolecule #1: MDH-tetramer in docking complex (MDH)4-(Pex5)1-(Pex14)1

SupramoleculeName: MDH-tetramer in docking complex (MDH)4-(Pex5)1-(Pex14)1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)

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Macromolecule #1: MDH tetramer in docking complex

MacromoleculeName: MDH tetramer in docking complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVNVAVIGAA GGIGQSLSLL LLRELPFGST LSLYDVVGAP GVAADLSHID RAGITVKHAA GKLPPVPRDP ALTELAEGVD VFVIVAGVPR KPGMTRDDLF NVNAGIVMDL VLTCASVSPN ACFCIVTNPV NSTTPIAAQT LRKIGVYNKN KLLGVSLLDG LRATRFINNA ...String:
MVNVAVIGAA GGIGQSLSLL LLRELPFGST LSLYDVVGAP GVAADLSHID RAGITVKHAA GKLPPVPRDP ALTELAEGVD VFVIVAGVPR KPGMTRDDLF NVNAGIVMDL VLTCASVSPN ACFCIVTNPV NSTTPIAAQT LRKIGVYNKN KLLGVSLLDG LRATRFINNA RHPLVVPYVP VVGGHSDVTI VPLYSQIPGP LPDESTLKEI RKRVQVAGTE VVKAKAGRGS ATLSMAEAGA RFTMHVVKAL MGLDTPMVYA YVDTDGEHEC PFLAMPVVLG KNGIERRLPI GPITTVEKEM LEEAVGVVKK NIAKGETFAR SKL

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 482240
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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