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- EMDB-8084: The structure of microsomal glutathione transferase 1 in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8084
TitleThe structure of microsomal glutathione transferase 1 in complex with Meisenheimer complex
Map dataNone
Sample
  • Complex: The structure of microsomal glutathione transferase 1 in complex with the Meisenheimer complex
    • Protein or peptide: Microsomal glutathione S-transferase 1
  • Ligand: 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PALMITIC ACID
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 / response to organonitrogen compound / apical part of cell / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane / identical protein binding
Similarity search - Function
Microsomal glutathione S-transferase 1-like / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family
Similarity search - Domain/homology
Microsomal glutathione S-transferase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodelectron crystallography / cryo EM / Resolution: 3.5 Å
AuthorsKuang Q / Purhonen P / Jegerschold C / Morgenstern R / Hebert H
CitationJournal: Sci Rep / Year: 2017
Title: Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation.
Authors: Qie Kuang / Pasi Purhonen / Johan Ålander / Richard Svensson / Veronika Hoogland / Jens Winerdal / Linda Spahiu / Astrid Ottosson-Wadlund / Caroline Jegerschöld / Ralf Morgenstern / Hans Hebert /
Abstract: Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used ...Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two aliphatic chains and one glutathione (GSH) molecule. The functional unit is a homotrimer centered on the crystallographic three-fold axes of the unit cell. The GSH substrate binds in an extended conformation at the interface between two subunits of the trimer supported by new in vitro mutagenesis data. Mutation of Arginine 130 to alanine resulted in complete loss of activity consistent with a role for Arginine 130 in stabilizing the strongly nucleophilic GSH thiolate required for catalysis. Based on the new model and an electron diffraction data set from crystals soaked with trinitrobenzene, that forms a dead-end Meisenheimer complex with GSH, a difference map was calculated. The map reveals side chain movements opening a cavity that defines the second substrate site.
History
DepositionFeb 21, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseJul 12, 2017-
UpdateMar 28, 2018-
Current statusMar 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.278
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.278
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ia9
  • Surface level: 0.278
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ia9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8084.png

Downloads & links

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Map

FileDownload / File: emd_8084.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.19 Å/pix.
x 84 pix.
= 100.002 Å		1.14 Å/pix.
x 73 pix.
= 81.799 Å		1.14 Å/pix.
x 73 pix.
= 81.799 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.1361 Å / Y: 1.1361 Å / Z: 1.1905 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.278 / Movie #1: 0.278
Minimum - Maximum-0.80948466 - 0.9331639
Average (Standard dev.)0.00009035481 (±0.13799676)
SymmetrySpace group: 168
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin00-41
Dimensions737384
Spacing727284
CellA: 81.7992 Å / B: 81.7992 Å / C: 100.002 Å
α: 90.0 ° / β: 90.0 ° / γ: 120.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.13609722222221.13609722222221.1905
M x/y/z727284
origin x/y/z0.0000.0000.000
length x/y/z81.79981.799100.002
α/β/γ90.00090.000120.000
start NX/NY/NZ00-41
NX/NY/NZ737384
MAP C/R/S213
start NC/NR/NS00-41
NC/NR/NS737384
D min/max/mean-0.8090.9330.000

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Supplemental data

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Sample components

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Entire : The structure of microsomal glutathione transferase 1 in complex ...

EntireName: The structure of microsomal glutathione transferase 1 in complex with the Meisenheimer complex
Components
  • Complex: The structure of microsomal glutathione transferase 1 in complex with the Meisenheimer complex
    • Protein or peptide: Microsomal glutathione S-transferase 1
  • Ligand: 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PALMITIC ACID

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Supramolecule #1: The structure of microsomal glutathione transferase 1 in complex ...

SupramoleculeName: The structure of microsomal glutathione transferase 1 in complex with the Meisenheimer complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pSP19T7LT
Molecular weightTheoretical: 543.57 KDa

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Macromolecule #1: Microsomal glutathione S-transferase 1

MacromoleculeName: Microsomal glutathione S-transferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 17.492488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADLKQLMDN EVLMAFTSYA TIILAKMMFL SSATAFQRLT NKVFANPEDC AGFGKGENAK KFLRTDEKVE RVRRAHLNDL ENIVPFLGI GLLYSLSGPD LSTALIHFRI FVGARIYHTI AYLTPLPQPN RGLAFFVGYG VTLSMAYRLL RSRLYL

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Macromolecule #2: 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE

MacromoleculeName: 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GTD
Molecular weightTheoretical: 520.428 Da
Chemical component information

ChemComp-GTD:
1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE

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Macromolecule #3: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

BufferpH: 7.4
Sugar embeddingMaterial: trehalose
VitrificationCryogen name: NITROGEN
Crystal formationLipid protein ratio: 3 / Lipid mixture: bovine liver lecithin / Temperature: 303.0 K / Details: dialysis

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Electron microscopy

MicroscopeJEOL 2100F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 200 mm
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 1.0 e/Å2

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Image processing

Crystal parametersUnit cell - A: 81.8 Å / Unit cell - B: 81.8 Å / Unit cell - C: 100.0 Å / Unit cell - γ: 120.0 ° / Plane group: P 6
Crystallography statisticsNumber intensities measured: 43603 / Number structure factors: 3063 / Fourier space coverage: 72.4 / R sym: 12 / R merge: 34.3 / Overall phase error: 0.0001 / Overall phase residual: 0.0001 / Phase error rejection criteria: 0 / High resolution: 3.5 Å
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES

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