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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


malate dehydrogenase / 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
CitationJournal: 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-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing 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
Brightness
Contrast
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

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: 0.117
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50339_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 : 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: malate dehydrogenase
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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