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- EMDB-31715: Cryo-EM Structure of Camellia sinensis glutamine synthetase CsGSI... -

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Basic information

Entry
Database: EMDB / ID: EMD-31715
TitleCryo-EM Structure of Camellia sinensis glutamine synthetase CsGSIb inactive Pentamer State III
Map dataCsGS1b Pen State III
Sample
  • Cell: CsGS1b
    • Protein or peptide: Glutamine synthetase
Keywordssupramolecular enzyme / glutamine synthetase / Camellia sinensis / PLANT PROTEIN / IMMUNE SYSTEM
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, beta-Grasp domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain ...: / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesCamellia sinensis (black tea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31715.png

Downloads & links

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Map

FileDownload / File: emd_31715.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCsGS1b Pen State III
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: 0.065
Minimum - Maximum-0.62317705 - 0.9410184
Average (Standard dev.)-0.0008402193 (±0.016871564)
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 : CsGS1b

EntireName: CsGS1b
Components
  • Cell: CsGS1b
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: CsGS1b

SupramoleculeName: CsGS1b / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Camellia sinensis (black tea)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Camellia sinensis (black tea)
Molecular weightTheoretical: 39.28918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLLSDLCNL NLSESTEKII AEYIWIGGSG MDLRSKARTL NAPVSDPSKL PQWNYDGSST GQAPGEDSEV ILYPQAIYKD PFRRGNNIL VMCDAYTPGG EPIPTNKRFD AAKIFSHPDV VAEEPWYGIE QEYTLLQKEV KWPIGWPVGG YPGPQGPYYC G IGADKAFG ...String:
MSLLSDLCNL NLSESTEKII AEYIWIGGSG MDLRSKARTL NAPVSDPSKL PQWNYDGSST GQAPGEDSEV ILYPQAIYKD PFRRGNNIL VMCDAYTPGG EPIPTNKRFD AAKIFSHPDV VAEEPWYGIE QEYTLLQKEV KWPIGWPVGG YPGPQGPYYC G IGADKAFG RDIVDAHYKA CLYAGINISG INGEVMPGQW EFQVGPSVGI SSGDQLWMAR YILERITEIA GVVVSFDPKP IE GDWNGAG AHTNYSTKSM RSDGGFEVIK KAIEKLGLKH REHIAAYGEG NERRLTGKHE TADINTFLWG VANRGASIRV GRD TEKAGK GYFEDRRPAS NMDPYIVTSM IANTTILWKP

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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90660
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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