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- EMDB-50340: Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50340
TitleCryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex
Map data
Sample
  • Complex: Ternary complex of (MDH)4 with PEX5
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor
KeywordsPeroxisomal protein transport / Cargo-Receptor complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


intracellular organelle lumen / peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / peroxisomal membrane / tricarboxylic acid cycle / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / Malate dehydrogenase, type 1 / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. ...PEX5/PEX5L / Malate dehydrogenase, type 1 / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
malate dehydrogenase / Peroxisome targeting signal 1 receptor
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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_50340.png

Downloads & links

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Map

FileDownload / File: emd_50340.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 296 pix.
= 248.64 Å		0.84 Å/pix.
x 296 pix.
= 248.64 Å		0.84 Å/pix.
x 296 pix.
= 248.64 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0809
Minimum - Maximum-1.1485864 - 1.7755129
Average (Standard dev.)0.00048992666 (±0.043927714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 248.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50340_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_50340_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 : Ternary complex of (MDH)4 with PEX5

EntireName: Ternary complex of (MDH)4 with PEX5
Components
  • Complex: Ternary complex of (MDH)4 with PEX5
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor

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Supramolecule #1: Ternary complex of (MDH)4 with PEX5

SupramoleculeName: Ternary complex of (MDH)4 with PEX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 231 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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Macromolecule #2: Peroxisome targeting signal 1 receptor

MacromoleculeName: Peroxisome targeting signal 1 receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 75.299586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHMD CSTGAAIGQQ FAKDAFHMHG GVGVGPTGNS EHDVLMNEMM MVQTPTGPAG EWTHQFAAYQ GQQQQQQQQH PQELAMRHQ QNDAFMLRQQ QEMEEAFCTF CTTHPHSHAH SHQPQGLVGP AMMGPQIMPP MMFGPGTGGF MMGAPPMMPY A SMKFAGDA ...String:
MAHHHHHHMD CSTGAAIGQQ FAKDAFHMHG GVGVGPTGNS EHDVLMNEMM MVQTPTGPAG EWTHQFAAYQ GQQQQQQQQH PQELAMRHQ QNDAFMLRQQ QEMEEAFCTF CTTHPHSHAH SHQPQGLVGP AMMGPQIMPP MMFGPGTGGF MMGAPPMMPY A SMKFAGDA AMAAANNTNM TQGATATSTT SVQQELQQQS SDNGWVEKLR DAEWAQDYSD AQVFTLEGQS EQTMEEHAKN SE FYQFMDK IRSKELLIDE ETGQLVQGPG PDPDAPEDAE YLKEWAAAEG LNMPPGFFEH MMQRPQGNNE QAEGRLFDGS NDA LMDDGA LDNAADVEEW VREYAEAQEQ LQRVQNETNY PFEPNNPYMY HDKPMEEGIA MLQLANMAEA ALAFEAVCQK EPEN VEAWR RLGTTQAENE KDCLAIIALN HARMLDPKDI AVHAALAVSH TNEHNVGAAL QSLRSWLLSQ PQYEHLGLVD LREVA ADEG LDEVPEENYF FAAPSEYRDC CTLLYAAVEM NPNDPQLHAS LGVLHNLSHR FDEAAKNFRR AVELRPDDAH MWNKLG ATL ANGNRPQEAL EAYNRALDIN PGYVRVMYNM AVSYSNMAQY PLAAKHITRA IALQAGGTNP QGEGSRIATR GLWDLLR MT LNLMDRSDLV EASWQQDLTP FLREFGLEEM AV

UniProtKB: Peroxisome targeting signal 1 receptor

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.79 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.38 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:

8ggh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538505
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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