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Yorodumi- PDB-2h8a: Structure of Microsomal Glutathione Transferase 1 in Complex with... -
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-Basic information
Entry | Database: PDB / ID: 2h8a | ||||||
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Title | Structure of Microsomal Glutathione Transferase 1 in Complex with Glutathione | ||||||
Components | Microsomal glutathione S-transferase 1 | ||||||
Keywords | TRANSFERASE / Membrane protein | ||||||
Function / homology | Function and homology information cellular response to lipid hydroperoxide / Aflatoxin activation and detoxification / glutathione transport / Glutathione conjugation / glutathione binding / Leydig cell differentiation / glutathione peroxidase activity / peroxisomal membrane / Neutrophil degranulation / glutathione transferase ...cellular response to lipid hydroperoxide / Aflatoxin activation and detoxification / glutathione transport / Glutathione conjugation / glutathione binding / Leydig cell differentiation / glutathione peroxidase activity / peroxisomal membrane / Neutrophil degranulation / glutathione transferase / glutathione transferase activity / : / glutathione metabolic process / apical part of cell / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Hebert, H. | ||||||
Citation | Journal: J Mol Biol / Year: 2006 Title: Structural basis for detoxification and oxidative stress protection in membranes. Authors: Peter J Holm / Priyaranjan Bhakat / Caroline Jegerschöld / Nobuhiko Gyobu / Kaoru Mitsuoka / Yoshinori Fujiyoshi / Ralf Morgenstern / Hans Hebert / Abstract: Synthesis of mediators of fever, pain and inflammation as well as protection against reactive molecules and oxidative stress is a hallmark of the MAPEG superfamily (membrane associated proteins in ...Synthesis of mediators of fever, pain and inflammation as well as protection against reactive molecules and oxidative stress is a hallmark of the MAPEG superfamily (membrane associated proteins in eicosanoid and glutathione metabolism). The structure of a MAPEG member, rat microsomal glutathione transferase 1, at 3.2 A resolution, solved here in complex with glutathione by electron crystallography, defines the active site location and a cytosolic domain involved in enzyme activation. The glutathione binding site is found to be different from that of the canonical soluble glutathione transferases. The architecture of the homotrimer supports a catalytic mechanism involving subunit interactions and reveals both cytosolic and membraneous substrate entry sites, providing a rationale for the membrane location of the enzyme. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2h8a.cif.gz | 37 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h8a.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 2h8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h8a_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 2h8a_full_validation.pdf.gz | 469.1 KB | Display | |
Data in XML | 2h8a_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 2h8a_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/2h8a ftp://data.pdbj.org/pub/pdb/validation_reports/h8/2h8a | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 17361.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P08011, glutathione transferase |
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#2: Chemical | ChemComp-GSH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Microsomal Glutathione Transferase 1 in Complex with Glutathione Type: COMPLEX / Details: Embedded in trehalose |
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Buffer solution | Name: potassium phosphate / pH: 8 / Details: potassium phosphate |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Carbon coated Mo-grids |
-Data collection
Microscopy | Model: JEOL 3000SFF / Details: Electron diffraction at 1.2 m camera length |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm / Cs: 1.6 mm |
Specimen holder | Temperature: 4 K / Tilt angle max: 62.6 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 e/Å2 Details: Kodak SO163 film for images, CCD for electron diffraction patterns |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Details: Crystallographic | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: Crystallographic / Resolution: 3.2 Å / Nominal pixel size: 1.17 Å Magnification calibration: Gold electron diffraction to establish exact unit cell parameters Symmetry type: 2D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.2→10 Å / Cor.coef. Fo:Fc: 0.619 / Cor.coef. Fo:Fc free: 0.356 / SU B: 29.134 / SU ML: 0.54 / Cross valid method: THROUGHOUT / ESU R: 1.747 / ESU R Free: 0.635 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.662 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
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