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- EMDB-31711: Cryo-EM Structure of Glycine max glutamine synthetase GmGS Beta2 -

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Basic information

Entry
Database: EMDB / ID: EMD-31711
TitleCryo-EM Structure of Glycine max glutamine synthetase GmGS Beta2
Map dataGmGS Beta2
Sample
  • Cell: GmGS Beta2
    • Protein or peptide: Glutamine synthetase
Keywordssupramolecular enzyme / glutamine synthetase / Glycine max / PLANT PROTEIN / LIGASE
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / cytoplasm
Similarity search - Function
: / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain ...: / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesGlycine max (soybean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsXu W / Chen Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2021
Title: Assembly status transition offers an avenue for activity modulation of a supramolecular enzyme.
Authors: Yao Chen / Weiya Xu / Shuwei Yu / Kang Ni / Guangbiao She / Xiaodong Ye / Qiong Xing / Jian Zhao / Chengdong Huang /
Abstract: Nature has evolved many supramolecular proteins assembled in certain, sometimes even seemingly oversophisticated, morphological manners. The rationale behind such evolutionary efforts is often poorly ...Nature has evolved many supramolecular proteins assembled in certain, sometimes even seemingly oversophisticated, morphological manners. The rationale behind such evolutionary efforts is often poorly understood. Here, we provide atomic-resolution insights into how the dynamic building of a structurally complex enzyme with higher order symmetry offers amenability to intricate regulation. We have established the functional coupling between enzymatic activity and protein morphological states of glutamine synthetase (GS), an old multi-subunit enzyme essential for cellular nitrogen metabolism. Cryo-EM structure determination of GS in both the catalytically active and inactive assembly states allows us to reveal an unanticipated self-assembly-induced disorder-order transition paradigm, in which the remote interactions between two subcomplex entities significantly rigidify the otherwise structurally fluctuating active sites, thereby regulating activity. We further show in vivo evidences that how the enzyme morphology transitions could be modulated by cellular factors on demand. Collectively, our data present an example of how assembly status transition offers an avenue for activity modulation, and sharpens our mechanistic understanding of the complex functional and regulatory properties of supramolecular enzymes.
History
DepositionAug 13, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31711.png

Downloads & links

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Map

FileDownload / File: emd_31711.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGmGS Beta2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 512 pix.
= 258.56 Å		0.51 Å/pix.
x 512 pix.
= 258.56 Å		0.51 Å/pix.
x 512 pix.
= 258.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.505 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.31389523 - 0.48451823
Average (Standard dev.)0.00023070679 (±0.01750452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 258.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GmGS Beta2

EntireName: GmGS Beta2
Components
  • Cell: GmGS Beta2
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: GmGS Beta2

SupramoleculeName: GmGS Beta2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glycine max (soybean)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Glycine max (soybean)
Molecular weightTheoretical: 39.184859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLLSDLINL NLSDTTEKVI AEYIWIGGSG MDLRSKARTL PGPVSDPSKL PKWNYDGSST GQAPGEDSEV IIYPQAIFRD PFRRGNNIL VICDTYTPAG EPIPTNKRHD AAKVFSHPDV VAEETWYGIE QEYTLLQKDI QWPLGWPVGG FPGPQGPYYC G VGADKAFG ...String:
MSLLSDLINL NLSDTTEKVI AEYIWIGGSG MDLRSKARTL PGPVSDPSKL PKWNYDGSST GQAPGEDSEV IIYPQAIFRD PFRRGNNIL VICDTYTPAG EPIPTNKRHD AAKVFSHPDV VAEETWYGIE QEYTLLQKDI QWPLGWPVGG FPGPQGPYYC G VGADKAFG RDIVDAHYKA CLYAGINISG INGEVMPGQW EFQVGPSVGI SAGDEVWAAR YILERITEIA GVVVSFDPKP IQ GDWNGAG AHTNYSTKSM RNDGGYEVIK TAIEKLGKRH KEHIAAYGEG NERRLTGRHE TADINTFLWG VANRGASVRV GRD TEKAGK GYFEDRRPAS NMDPYVVTSM IADTTILWKP

UniProtKB: Glutamine synthetase

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104717
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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