+Open data
-Basic information
Entry | Database: PDB / ID: 8gi0 | |||||||||
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Title | Structure of Trypanosoma docking complex | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Peroxisomal transport / Import / PEX / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information peroxisome matrix targeting signal-1 binding / peroxisomal importomer complex / protein import into peroxisome matrix, docking / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / peroxisomal membrane / tricarboxylic acid cycle / signaling receptor binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) Trypanosoma cruzi strain CL Brener (eukaryote) Trypanosoma cruzi cruzi (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Sonani, R.R. / Artur, B. / Jemiola-Rzeminska, M. / Lipinski, O. / Patel, S.N. / Sood, T. / Dubin, G. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: To Be Published Title: Structure of Trypanosoma docking complex Authors: Sonani, R.R. / Dubin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gi0.cif.gz | 304.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gi0.ent.gz | 241 KB | Display | PDB format |
PDBx/mmJSON format | 8gi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gi0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8gi0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8gi0_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 8gi0_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/8gi0 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8gi0 | HTTPS FTP |
-Related structure data
Related structure data | 40056MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 40507.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_80g13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2WKZ5 | ||
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#2: Protein | Mass: 34106.832 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 BL21(DE3) (bacteria) / References: UniProt: Q4DRD8 #3: Protein | | Mass: 74268.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi cruzi (eukaryote) / Gene: TCDM_08436 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5B7T1 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 482240 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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