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- PDB-9fef: Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex -

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Basic information

Entry
Database: PDB / ID: 9fef
TitleCryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex
Components
  • Peroxisome targeting signal 1 receptor
  • malate dehydrogenase
KeywordsTRANSPORT PROTEIN / Peroxisomal protein transport / Cargo-Receptor complex
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / peroxisome
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLipinski, O. / Sonani, R.R. / Blat, A. / Jemiola-Rzeminska, M. / Patel, S.N. / Sood, T. / Dubin, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: To Be Published
Title: Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex
Authors: Lipinski, O. / Sonani, R.R. / Blat, A. / Jemiola-Rzeminska, M. / Patel, S.N. / Sood, T. / Dubin, G.
History
DepositionMay 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: malate dehydrogenase
B: malate dehydrogenase
C: malate dehydrogenase
D: malate dehydrogenase
E: Peroxisome targeting signal 1 receptor


Theoretical massNumber of molelcules
Total (without water)215,8525
Polymers215,8525
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
malate dehydrogenase


Mass: 35137.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Gene: Tc00.1047053506503.69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DRD8, malate dehydrogenase
#2: Protein Peroxisome targeting signal 1 receptor


Mass: 75299.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Gene: TCDM_08436 / Production host: Escherichia coli (E. coli) / References: UniProt: V5B7T1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of (MDH)4 with PEX5 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.231 MDa / Experimental value: NO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3380 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 42.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 538505 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811379
ELECTRON MICROSCOPYf_angle_d0.74915488
ELECTRON MICROSCOPYf_dihedral_angle_d5.1661595
ELECTRON MICROSCOPYf_chiral_restr0.0431873
ELECTRON MICROSCOPYf_plane_restr0.0062002

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