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- EMDB-50339: Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-50339
TitleCryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase
Map data
Sample
  • Complex: Tetrameric complex of glycosomal malate dehydrogenase
    • Protein or peptide: malate dehydrogenase
KeywordsOxidoreductase / Tetramer / Metabolic enzyme
Function / homology
Function and homology information


intracellular organelle lumen / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1 / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
malate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLipinski O / Sonani RR / Blat A / Jemiola-Rzeminska M / Patel SN / Sood T / Dubin G
Funding support Poland, 3 items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
Polish National Science Centre2020/39/B/NZ1/01551 Poland
Citation
Journal: Nat Commun / Year: 2025
Title: Structure of Trypanosoma peroxisomal import complex unveils conformational heterogeneity.
Authors: Ravi R Sonani / Artur Blat / Malgorzata Jemiola-Rzeminska / Oskar Lipinski / Stuti N Patel / Tabassum Sood / Grzegorz Dubin /
Abstract: Peroxisomes are membrane enclosed organelles hosting diverse metabolic processes in eukaryotic cells. Having no protein synthetic abilities, peroxisomes import all required enzymes from the cytosol ...Peroxisomes are membrane enclosed organelles hosting diverse metabolic processes in eukaryotic cells. Having no protein synthetic abilities, peroxisomes import all required enzymes from the cytosol through a peroxin (Pex) import system. Peroxisome targeting sequence 1 (PTS1)-tagged cargo is recognized by cytosolic receptor, Pex5. The cargo-Pex5 complex docks at the peroxisomal membrane translocon, composed of Pex14 and Pex13, facilitating translocation into the peroxisomal lumen. Despite its significance, the structural basis of the process is only partially understood. Here, we characterize the cargo-Pex5-Pex14 ternary complex from Trypanosoma cruzi. Cryo-electron microscopy maps enabled model building for Pex5 (residues 327-462 and 487-653) bound to malate dehydrogenase (MDH; residues 1-323) cargo tetramer and Pex14 (residues 21-85). The model provides insight into conformational heterogeneity and identifies secondary interfaces. Specifically, we observe that orientations of Pex5 relative to MDH span a 17° angle. Additionally, PTS1- and Wxxx(F/Y)-independent contact surfaces are observed at MDH-Pex5 and Pex5-Pex14 interfaces, respectively. Mutational analysis indicates that the non-PTS1 MDH-Pex5 interface does not significantly contribute to the affinity, but limits the conformational heterogeneity of MDH-Pex5 interface. The Pex5-Pex14 interface constitutes an extended binding site of Pex14 over Pex5. We discuss the implications of these findings for understanding peroxisomal import mechanism.
#1: Journal: Biorxiv / Year: 2024
Title: Structure of Trypanosoma peroxisomal import complex unveils conformational dynamics
Authors: Sonani RR / Blat A / Jemiola-Rzeminska M / Lipinski O / Patel SN / Sood T / Dubin G
History
DepositionMay 19, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50339.png

Downloads & links

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Map

FileDownload / File: emd_50339.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 220 pix.
= 189.2 Å		0.86 Å/pix.
x 220 pix.
= 189.2 Å		0.86 Å/pix.
x 220 pix.
= 189.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.49765375 - 0.8334843
Average (Standard dev.)0.001599747 (±0.032842737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 189.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50339_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50339_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric complex of glycosomal malate dehydrogenase

EntireName: Tetrameric complex of glycosomal malate dehydrogenase
Components
  • Complex: Tetrameric complex of glycosomal malate dehydrogenase
    • Protein or peptide: malate dehydrogenase

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Supramolecule #1: Tetrameric complex of glycosomal malate dehydrogenase

SupramoleculeName: Tetrameric complex of glycosomal malate dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: malate dehydrogenase

MacromoleculeName: malate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 35.13798 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHMV NVAVIGAAGG IGQSLSLLLL RELPFGSTLS LYDVVGAPGV AADLSHIDRA GITVKHAAGK LPPVPRDPAL TELAEGVDV FVIVAGVPRK PGMTRDDLFN VNAGIVMDLV LTCASVSPNA CFCIVTNPVN STTPIAAQTL RKIGVYNKNK L LGVSLLDG ...String:
MAHHHHHHMV NVAVIGAAGG IGQSLSLLLL RELPFGSTLS LYDVVGAPGV AADLSHIDRA GITVKHAAGK LPPVPRDPAL TELAEGVDV FVIVAGVPRK PGMTRDDLFN VNAGIVMDLV LTCASVSPNA CFCIVTNPVN STTPIAAQTL RKIGVYNKNK L LGVSLLDG LRATRFINNA RHPLVVPYVP VVGGHSDVTI VPLYSQIPGP LPDESTLKEI RKRVQVAGTE VVKAKAGRGS AT LSMAEAG ARFTMHVVKA LMGLDTPMVY AYVDTDGEHE CPFLAMPVVL GKNGIERRLP IGPITTVEKE MLEEAVGVVK KNI AKGETF ARSKL

UniProtKB: malate dehydrogenase

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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: 8
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7qoz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 312103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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