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Yorodumi- PDB-6xod: Crystal structure of the PEX4-PEX22 protein complex from Arabidop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xod | |||||||||||||||||||||
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Title | Crystal structure of the PEX4-PEX22 protein complex from Arabidopsis thaliana | |||||||||||||||||||||
Components |
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Keywords | LIGASE/TRANSPORT PROTEIN / peroxin / E2 / ubiquitin-conjugating enzyme / LIGASE / TRANSFERASE / LIGASE-TRANSPORT PROTEIN complex | |||||||||||||||||||||
Function / homology | Function and homology information protein import into peroxisome matrix / peroxisome organization / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / fatty acid beta-oxidation / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / protein transport / membrane => GO:0016020 ...protein import into peroxisome matrix / peroxisome organization / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / fatty acid beta-oxidation / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / protein transport / membrane => GO:0016020 / protein ubiquitination / ATP binding / nucleus Similarity search - Function | |||||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | |||||||||||||||||||||
Authors | Olmos Jr., J.L. / Bradford, S.E. / Miller, M.D. / Xu, W. / Wright, Z.J. / Bartel, B. / Phillips Jr., G.N. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Front Cell Dev Biol / Year: 2022 Title: The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane Authors: Traver, M.S. / Bradford, S.E. / Olmos, J.L. / Wright, Z.J. / Miller, M.D. / Xu, W. / Phillips, G.N. / Bartel, B. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xod.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xod.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xod_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 6xod_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 6xod_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 6xod_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/6xod ftp://data.pdbj.org/pub/pdb/validation_reports/xo/6xod | HTTPS FTP |
-Related structure data
Related structure data | 5nkzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18546.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PEX4, UBC21, At5g25760, F18A17.10 / Plasmid: pET-6XHIS-MBP-LIC-cloning-PEX4-PEX22-XLlinker Details (production host): expressed as a chimera with MBP and PEX22 and was cleaved with TEV and Precission Proteases to form the final products Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8LGF7, E2 ubiquitin-conjugating enzyme |
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#2: Protein | Mass: 19676.396 Da / Num. of mol.: 1 / Fragment: Cytosolic domain, residues 111-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PEX22, At3g21865, MSD21.24 / Plasmid: pET-6XHIS-MBP-LIC-cloning-PEX4-PEX22-XLlinker Details (production host): expressed as a chimera with MBP and PEX4 and was cleaved with TEV and Precission Proteases to form the final products Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LSX7 |
#3: Water | ChemComp-HOH / |
Sequence details | The construct was expressed as a fusion with an N-terminal TEV-cleavable 6-His MBP tag, the PEX 4 ...The construct was expressed as a fusion with an N-terminal TEV-cleavable 6-His MBP tag, the PEX 4 (residues 1-157), a linker containing a precision protease site (LEVLFQ/GP) and cytosolic domain of PEX 22 (residues 111-283 - lacking the predicted N-terminal luminal tail, transmembrane domain and unstructured tether). After purification, the N-terminal tag was removed with TEV-protease and the linker between PEX-4 and PEX-22 was cleaved with PreScission protease leaving the PEX-4 with an S remaining at the N-terminus after cleavage with TEV-protease and LEVLFQ from the linker at the C-terminus after cleavage with precision protease. The PEX-22(111-283) construct retains GP from the linker at its N-termius after cleavage. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 100 mM NaCl, 100 mM Bis-Tris Propane, 25% (w/v) PEG 1,500 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.008→56.046 Å / Num. obs: 22014 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NKZ Resolution: 2.01→49.83 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 273 Å2 / Biso mean: 61.9435 Å2 / Biso min: 26.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→49.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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