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Yorodumi- PDB-5u3c: CryoEM structure of the CTP synthase filament at 4.6 Angstrom res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u3c | ||||||
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Title | CryoEM structure of the CTP synthase filament at 4.6 Angstrom resolution | ||||||
Components | CTP synthase | ||||||
Keywords | PROTEIN FIBRIL / LIGASE / nucleotide metabolism / metabolic filament | ||||||
Function / homology | Function and homology information CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding ...CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Kollman, J.M. / Lynch, E.M. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Human CTP synthase filament structure reveals the active enzyme conformation. Authors: Eric M Lynch / Derrick R Hicks / Matthew Shepherd / James A Endrizzi / Allison Maker / Jesse M Hansen / Rachael M Barry / Zemer Gitai / Enoch P Baldwin / Justin M Kollman / Abstract: The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we ...The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we show that for human CTPS, polymerization increases catalytic activity. The cryo-EM structures of bacterial and human CTPS filaments differ considerably in overall architecture and in the conformation of the CTPS protomer, explaining the divergent consequences of polymerization on activity. The structure of human CTPS filament, the first structure of the full-length human enzyme, reveals a novel active conformation. The filament structures elucidate allosteric mechanisms of assembly and regulation that rely on a conserved conformational equilibrium. The findings may provide a mechanism for increasing human CTPS activity in response to metabolic state and challenge the assumption that metabolic filaments are generally storage forms of inactive enzymes. Allosteric regulation of CTPS polymerization by ligands likely represents a fundamental mechanism underlying assembly of other metabolic filaments. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5u3c.cif.gz | 762.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u3c.ent.gz | 658.6 KB | Display | PDB format |
PDBx/mmJSON format | 5u3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u3c_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5u3c_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5u3c_validation.xml.gz | 60.7 KB | Display | |
Data in CIF | 5u3c_validation.cif.gz | 89.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/5u3c ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u3c | HTTPS FTP |
-Related structure data
Related structure data | 8504MC 8474C 8475C 8476C 8490C 8491C 8513C 5tkvC 5u03C 5u05C 5u6rC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 7 / Rise per n subunits: 81.591 Å / Rotation per n subunits: 48.563 °) |
-Components
#1: Protein | Mass: 60446.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrG, ECS88_3048 / Production host: Escherichia coli (E. coli) References: UniProt: B7MLA1, UniProt: P0A7E5*PLUS, CTP synthase (glutamine hydrolysing) #2: Chemical | ChemComp-CTP / #3: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: CTP synthase filament / Type: COMPLEX Details: CTP synthase was incubated in the presence of substrates, and filaments form as the product CTP builds up in the reaction. Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pET22 |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 0.85 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: E. coli CTP synthase bound to CTP and ADP |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 34 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Helical symmerty | Angular rotation/subunit: 48.5 ° / Axial rise/subunit: 81.6 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8622 / Symmetry type: HELICAL |