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Open data
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Basic information
Entry | Database: PDB / ID: 8gh3 | |||||||||
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Title | Structure of Trypanosoma (MDH)4-(Pex5)2, distal conformation | |||||||||
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![]() | TRANSPORT PROTEIN / Peroxisomal transport / Trypanosoma / Import / PEX | |||||||||
Function / homology | ![]() 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||
![]() | Sonani, R.R. / Artur, B. / Jemiola-Rzeminska, M. / Lipinski, O. / Patel, S.N. / Sood, T. / Dubin, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Trypanosoma (MDH)4-(Pex5)2, distal conformation Authors: Sonani, R.R. / Dubin, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 307.7 KB | Display | ![]() |
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PDB format | ![]() | 247.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 40032MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 34106.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Tc00.1047053506503.69 / Production host: ![]() ![]() #2: Protein | Mass: 74268.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Complex of MDH-tetramer and PEX5 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 42.25 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12554 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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