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Yorodumi- PDB-7zbn: Cryo-EM structure of the human GS-GN complex in the inhibited state -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zbn | ||||||
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Title | Cryo-EM structure of the human GS-GN complex in the inhibited state | ||||||
Components |
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Keywords | TRANSFERASE / Glycosyltransferase | ||||||
Function / homology | Function and homology information glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding ...glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / inclusion body / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / heart development / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å | ||||||
Authors | Marr, L. / Zeqiraj, E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Mechanism of glycogen synthase inactivation and interaction with glycogenin. Authors: Laura Marr / Dipsikha Biswas / Leonard A Daly / Christopher Browning / Sarah C M Vial / Daniel P Maskell / Catherine Hudson / Jay A Bertrand / John Pollard / Neil A Ranson / Heena Khatter / ...Authors: Laura Marr / Dipsikha Biswas / Leonard A Daly / Christopher Browning / Sarah C M Vial / Daniel P Maskell / Catherine Hudson / Jay A Bertrand / John Pollard / Neil A Ranson / Heena Khatter / Claire E Eyers / Kei Sakamoto / Elton Zeqiraj / Abstract: Glycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS) ...Glycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS), where GS is activated by glucose-6-phosphate (G6P) and inactivated by phosphorylation. We describe the 2.6 Å resolution cryo-EM structure of phosphorylated human GS revealing an autoinhibited GS tetramer flanked by two GN dimers. Phosphorylated N- and C-termini from two GS protomers converge near the G6P-binding pocket and buttress against GS regulatory helices. This keeps GS in an inactive conformation mediated by phospho-Ser641 interactions with a composite "arginine cradle". Structure-guided mutagenesis perturbing interactions with phosphorylated tails led to increased basal/unstimulated GS activity. We propose that multivalent phosphorylation supports GS autoinhibition through interactions from a dynamic "spike" region, allowing a tuneable rheostat for regulating GS activity. This work therefore provides insights into glycogen synthesis regulation and facilitates studies of glycogen-related diseases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zbn.cif.gz | 859.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zbn.ent.gz | 713.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zbn_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7zbn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7zbn_validation.xml.gz | 75.2 KB | Display | |
Data in CIF | 7zbn_validation.cif.gz | 107 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/7zbn ftp://data.pdbj.org/pub/pdb/validation_reports/zb/7zbn | HTTPS FTP |
-Related structure data
Related structure data | 14587MC 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: 83885.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GYS1, GYS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13807, glycogen(starch) synthase #2: Protein | Mass: 83965.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GYS1, GYS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13807, glycogen(starch) synthase #3: Protein | Mass: 37469.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GYG1, GYG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P46976, glycogenin glucosyltransferase Has ligand of interest | Y | |
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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: Glycogen synthase-Glycogenin complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.485 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 34.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 739232 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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