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Yorodumi- PDB-7v4i: Cryo-EM Structure of Camellia sinensis glutamine synthetase CsGSI... -
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-Basic information
Entry | Database: PDB / ID: 7v4i | ||||||
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Title | Cryo-EM Structure of Camellia sinensis glutamine synthetase CsGSIb decamer assembly | ||||||
Components | Glutamine synthetase | ||||||
Keywords | IMMUNE SYSTEM / supramolecular enzyme / glutamine synthetase / Camellia sinensis / PLANT PROTEIN | ||||||
Function / homology | Function and homology information glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Camellia sinensis (black tea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Xu, W. / Chen, Y. / Xing, Q. / Huang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 7v4i.cif.gz | 587.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v4i.ent.gz | 494.6 KB | Display | PDB format |
PDBx/mmJSON format | 7v4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v4i_validation.pdf.gz | 893.3 KB | Display | wwPDB validaton report |
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Full document | 7v4i_full_validation.pdf.gz | 936.5 KB | Display | |
Data in XML | 7v4i_validation.xml.gz | 92.7 KB | Display | |
Data in CIF | 7v4i_validation.cif.gz | 140.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/7v4i ftp://data.pdbj.org/pub/pdb/validation_reports/v4/7v4i | HTTPS FTP |
-Related structure data
Related structure data | 31712MC 7v4hC 7v4jC 7v4kC 7v4lC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39289.180 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camellia sinensis (black tea) / Gene: CsGS1;3, GS1.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q762D2, glutamine synthetase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CsGS1b / Type: CELL / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Glycine max (soybean) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 51 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43876 / Symmetry type: POINT | ||||||||||||||||||||||||
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