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- EMDB-2581: The structures of cytosolic and plastid-located glutamine synthet... -

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Basic information

Entry
Database: EMDB / ID: EMD-2581
TitleThe structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture
Map datagsii-a reconstruction from M. trucantula
Sample
  • Sample: gsii-a from M. trucantula
  • Protein or peptide: MtGSII-2a
Keywordsglutamine synthetases / Medicago trucantula
Biological speciesMedicago truncatula (barrel medic)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsTorreira E / Seabra AR / Marriott H / Zhou M / Llorca O / Robinson CV / Carvalho HG / Fernandez-Tornero C / Pereira PJB
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2014
Title: The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture.
Authors: Eva Torreira / Ana Rita Seabra / Hazel Marriott / Min Zhou / Óscar Llorca / Carol V Robinson / Helena G Carvalho / Carlos Fernández-Tornero / Pedro José Barbosa Pereira /
Abstract: The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily ...The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of crop yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.
History
DepositionFeb 18, 2014-
Header (metadata) releaseMar 19, 2014-
Map releaseApr 16, 2014-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2581.png

Downloads & links

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Map

FileDownload / File: emd_2581.map.gz / Format: CCP4 / Size: 20.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgsii-a reconstruction from M. trucantula
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 176 pix.
= 285.12 Å		1.62 Å/pix.
x 176 pix.
= 285.12 Å		1.62 Å/pix.
x 176 pix.
= 285.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0028 / Movie #1: 0.0012
Minimum - Maximum-0.00040951 - 0.00454528
Average (Standard dev.)0.0000854 (±0.0004523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-88-88-88
Dimensions176176176
Spacing176176176
CellA=B=C: 285.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z285.120285.120285.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS-88-88-88
NC/NR/NS176176176
D min/max/mean-0.0000.0050.000

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Supplemental data

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Sample components

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Entire : gsii-a from M. trucantula

EntireName: gsii-a from M. trucantula
Components
  • Sample: gsii-a from M. trucantula
  • Protein or peptide: MtGSII-2a

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Supramolecule #1000: gsii-a from M. trucantula

SupramoleculeName: gsii-a from M. trucantula / type: sample / ID: 1000 / Oligomeric state: 2-pentameric rings / Number unique components: 1
Molecular weightExperimental: 441 KDa / Theoretical: 440 KDa / Method: Native mass-spec

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Macromolecule #1: MtGSII-2a

MacromoleculeName: MtGSII-2a / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Oligomeric state: Decamer / Recombinant expression: Yes
Source (natural)Organism: Medicago truncatula (barrel medic) / synonym: Barrel medic / Location in cell: plastid
Molecular weightExperimental: 441 KDa / Theoretical: 440 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: CodonPlus RIL / Recombinant plasmid: pET-24-d(+)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4 / Details: 10 mM HEPES PH 7.4
GridDetails: Glow-discharged QUANTIFOIL R 2/2 holey grids
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeJEOL 2200FS
DateNov 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 83393 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe final reconstruction was determined employing just perfect side-views.
CTF correctionDetails: CTFFIND and BSOFT
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN1.9, Xmipp / Number images used: 3117

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Atomic model buiding 1

Initial modelPDB ID:

4is4

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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